I think I found John's family (along with other relatives?) in Florence, New York. But there were 2 John Courtney born about 1858-1859, each with a father Humphrey. Humphrey (born Ireland) and Ellen (born New York ), and Humphrey D. (born Ireland) and Johanna (born Ireland). The John with Humphrey and Ellen is gone from the 1880 census, and the John with Humphrey D. and Johanna is still with his parents, now living in Fitchburg, Worcester, Massachusetts. But by 1900, Humphrey and Johanna are back in Florence, New York. And it (looks like) the John, son of Humphrey and Ellen is also in Florence in 1900.
So, I am assuming that your John was most likely the son of Humphrey and Johanna, and that Humphrey may have been the son of Dennis Courtney. The other Humphrey (with Ellen) seems to have been a son of Humphrey Sr. So it's possible that the 2 oldest Courtneys, Dennis (born 1795?) and Humphrey (born 1800?), may have been brothers
All census records of John and Sarah from 1900 to 1930 in Appleton state that both of John's parents were born in Ireland
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1850 United States Federal Census
Home in 1850: Town of Florence, Oneida, New York, Enumerated August 15, Dwelling 29, Family 29, Lines 13-18
Humphrey Courtney, age 49, born abt 1801 Ireland
Catharine Courtney, age 40, born abt 1810 Ireland
John C Courtney, age 21, born abt 1829 Ireland
Humphrey Courtney, age 14, born abt 1836 Ireland
Michael Courtney, age 8, born abt 1842 Connecticut
Daniel Courtney, age 7, born abt 1843 Connecticut
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1850 United States Federal Census
Home in 1850: Town of Florence, Oneida, New York, Page 193, Enumerated August 15, Dwelling 41, Family 41, Lines 32-37
Dennis Courtney, age 57, born abt 1793 Ireland
Daniel Courtney, age 27, born abt 1823 Ireland
John Courtney, age 24, born abt 1826 Ireland
Humphrey Courtney, age 22, born abt 1828 Ireland
Bridget Courtney, age 19, born abt 1831 Ireland
Edmund Courtney, age 17, born abt 1833 Ireland
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1860 United States Federal Census
Home in 1860: Town of Florence, Oneida, New York, Page 47, Enumerated July 18, Dwelling 392, Family 369, Lines 25-29
Post Office: Florence
Humphry D Courtney, age 31, born abt 1829 Ireland
Johanna Courtney, age 24, born abt 1836 Ireland
Dennis Courtney, age 3, born abt 1857 New York
John Courtney, age 1, born abt 1859 New York
Dennis Courtney, boarder, age 67, born abt 1793 Ireland
SAME PAGE...NEXT FAMILY......
1860 United States Federal Census
Home in 1860: Town of Florence, Oneida, New York, Page 47, Enumerated July 18, Dwelling 393, Family 370, Lines 30-35
Post Office: Florence
Daniel Courtney, age 36, born abt 1824 Ireland
Margaret Courtney, age 27, born abt 1833 Ireland
Hannora Courtney, age 5, born abt 1855 New York
Catharine Courtney, age 3, born abt 1857 New York
John Courtney, age 2, born abt 1858 New York
Bridget Courtney, age 6.12, born abt 1859 New York
SAME PAGE...NEXT FAMILY......
1860 United States Federal Census
Home in 1860: Town of Florence, Oneida, New York, Page 47, Enumerated July 18, Dwelling 394, Family 371, Lines 36-40 + Next Page 48, Lines 1-4
Post Office: Florence
Humphry Courtney, age 61, born abt 1799 Ireland
Catharine Courtney, age 54, born abt 1806 Ireland
Humphry Jr. Courtney, age 22, born abt 1838 Ireland
Micheal Courtney, age 19? 16?, born abt 1841 or 1843 New York
Daniel Courtney, age 16, born abt 1844 New York
Ellen Courtney, age 22, born abt 1838 New York
John Courtney, age 2, born abt 1858 New York
Catharine Courtney 8.12, born abt 1859 New York
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1860 United States Federal Census
Home in 1860: Town of Florence, Oneida, New York, Page 11, Enumerated June 27, Dwelling 86, Family 77, Lines 30-34
Post Office: Florence
John Courtney, age 30, born abt 1830 Ireland
Mary Courtney, age 28, born abt 1832 Ireland
Kattie Courtney, age 4, born abt 1856 New York
Humphry Courtney, age 2, born abt 1858 New York
Mary A Courtney, age 8.12, born abt 1859 New York
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1870 United States Federal Census
Home in 1870: Town of Florence, Oneida, New York, Page 32, Enumerated June 24, Dwelling 272, Family 274, Lines 29-40 + Next Page 33, Line 1
Post Office: Stokes
Humphrey Courtney, age 34, born abt 1836 Ireland
Ellen Courtney, age 32, born abt 1838 New York
John Courtney, age 12, born abt 1858 New York
Catharine Courtney, age 10, born abt 1860 New York
Bridget Courtney, age 6, born abt 1864 New York
Michael Courtney, age 8, born abt 1862 New York
Patrick Courtney, age 4, born abt 1866 New York
Morris Courtney, age 1, born abt 1869 New York
Humphrey Courtney, age 75, born abt 1875 Ireland
Catharine Courtney, age 70, born abt 1800 Ireland
Catharine Courtney, age 23, born abt 1847 New York
Catharine Courtney, age 2, born abt 1868 New York
Humphrey Courtney, age 9/12, born abt 1869 New York
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1870 United States Federal Census
Home in 1870: Town of Florence, Oneida, New York, Page 41, Enumerated June 30, Dwelling 351, Family 351, Lines 29-35
Post Office: Stokes
Humphrey Courtney, age 40, born abt 1830 Ireland
Johannah Courtney, age 35, born abt 1835 Ireland
John Courtney, age 11, born abt 1859 New York
Giles Courtney, age 9, born abt 1861 New York
Hannorah Courtney, age 7, born abt 1863 New York
Mary Courtney, age 4, born abt 1866 New York
Bridget Courtney, age 2, born abt 1868 New York
NEXT FAMILY...Same Page......
1870 United States Federal Census
Home in 1870: Town of Florence, Oneida, New York, Page 41, Enumerated June 30, Dwelling 252 (352?), Family 252 (352?), Lines 36-40 + Next Page 42, Lines 1-4
Post Office: Stokes
Daniel Courtney, age 46, born abt 1824 Ireland
Margaret Courtney, age 32, born abt 1838 Ireland
Hannora Courtney, age 15, born abt 1855 New York
Catharine Courtney, age 14, born abt 1856 New York
Bridget Courtney, age 11, born abt 1859 New York
Ellen Courtney, age 10, born abt 1860 New York
Mary Courtney, age 5, born abt 1865 New York
Humphrey Courtney, age 3, born abt 1867 New York
James Courtney, age 1/12, born abt 1869 New York
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1870 United States Federal Census
Home in 1870: Town of Florence, Oneida, New York, Page 14, Enumerated June 18, Dwelling 114, Family 114, Lines 23-30
Post Office: Stokes
John Courtney, age 40, born abt 1830 Ireland
Mary Courtney, age 37, born abt 1833 Ireland
Catharine Courtney, age 14, born abt 1856 New York
Humphrey Courtney, age 12, born abt 1858 New York
Mary Courtney, age 10, born abt 1860 New York
Bridget Courtney, age 7, born abt 1863 New York
Michael Courtney, age 6, born abt 1864 New York
Daniel Courtney, age 3, born abt 1867 New York
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1880 United States Federal Census
Home in 1880: Florence, Oneida, New York, ED 91, Page 9A, Dwelling 84, Family 86, Lines 36-45
Humphrey Courtney, head, age 44, married, born abt 1836
Ireland, parents born Ireland
Ellen Courtney, wife, age 42, married, born abt 1838
New York, parents born Ireland
Michael Courtney, son, age 18, born abt 1862
New York, father born Ireland, mother born New York
Bridget Courtney, daughter, age 16, born abt 1864
New York, father born Ireland, mother born New York
Patrick Courtney, son, age 14, born abt 1866
New York, father born Ireland, mother born New York
Maurice Courtney, son, age 11, born abt 1869
New York, father born Ireland, mother born New York
Julie Courtney, daughter, age 7, born abt 1873
New York, father born Ireland, mother born New York
Humphrey Courtney, son, age 4, born abt 1876
New York, father born Ireland, mother born New York
Daniel Courtney, son, age 1, born abt 1879
New York, father born Ireland, mother born New York
Catharine Courtney, mother, age 80, widow, born abt 1800 Ireland, parents born Ireland
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SAME PAGE.....Just above Humphrey Courtney family
1880 United States Federal Census
Home in 1880: Florence, Oneida, New York, ED 91, Page 9A, Dwelling 83, Family 85, Lines 29-35
Daniel Courtney, head, age 54, married, born abt 1826
Ireland, parents born Ireland
Margaret Courtney, wife, age 40, married, born abt 1840
Ireland, parents born Ireland
John Courtney, son, age 22, born abt 1858
New York, parents born Ireland
Mary Courtney, daughter, age 16, born abt 1864
New York, parents born Ireland
Humphrey Courtney, son, age 14, born abt 1866
New York, parents born Ireland
James Courtney, son, age 12, born abt 1868
New York, parents born Ireland
Margaret Courtney, daughter, age 8, born abt 1872
New York, parents born Ireland
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1880 United States Federal Census
Home in 1880: Florence, Oneida, New York, ED 91, Page 12D, Dwelling 112, Family 116, Lines 35-37
John Courtney, head, age 60, widower, born abt 1820 Ireland, parents born Ireland
Bridget Courtney, daughter, age 16, born abt 1864
New York, parents born Ireland
Daniel Courtney, son, age 14, born abt 1866
New York, parents born Ireland
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1880 United States Federal Census
Home in 1880: Ward 2, City of Fitchburg, Worcester, Massachusetts , ED 875, Page 9A, Enumerated June 3, Dwelling 54, Family 74, Lines 2-8
Humphrey D. Courtney, head, age 51, born abt 1829 Ireland, parents born Ireland, Occupation: laborer
Johanna Courtney, wife, age 43, born abt 1837 Ireland, parents born Ireland
John Courtney, son, age 20, born abt 1860 New York, parents born Ireland, Occupation: Works in Woolen Mill
Giles Courtney, son, age 18, born abt 1862 New York, parents born Ireland, Occupation: Works in Woolen Mill
Nora Courtney, daughter, age 17, born abt 1863 New York, parents born Ireland, Occupation: Works in cotton Mill
Bridget Courtney, daughter, age 12, born abt 1868 New York, parents born Ireland
Margaret Courtney, daughter, age 2, born abt 1878 Massachusetts, parents born Ireland
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1900 United States Federal Census
Home in 1900: Florence, Oneida, New York, ED 15, Sheet 2B, Enumerated June 15, Dwelling 46, Family 46, Lines 79-82
Residence : Florence Township (North & East Part), Oneida, New York
Humphrey Courtney, head, age 64, widower, born Mar 1836
Ireland, parents born Ireland, immigration 1839
Julia Courtney, daughter, age 25, single, born Feb 1875
New York, father born Ireland, mother born New York
Daniel Courtney, son, age 21, single, born May 1878
New York, father born Ireland, mother born New York
Charles Courtney, son, age 18, single, born Feb 1882
New York, father born Ireland, mother born New York
SAME PAGE...NEXT FAMILY....
1900 United States Federal Census
Home in 1900: Florence, Oneida, New York, ED 15, Sheet 2B, Enumerated June 15, Dwelling 47, Family 47, Lines 83-84
Residence : Florence Township (North & East Part), Oneida, New York
John Courtney, head, age 44, single, born Nov 1855
New York, parents born Ireland
Margret Courtney, mother, age 75, widow, 1 child, 1 living, born Nov 1824 Ireland, parents born Ireland, immigrated 1825
SAME PAGE...4th family down from John and Margaret
1900 United States Federal Census
Home in 1900: Florence, Oneida, New York, ED 15, Sheet 2B, Enumerated June 15, Dwelling 51, Family 51, Lines 93-94
Residence : Florence Township (North & East Part), Oneida, New York
Humphrey Courtney, head, age 71, married 44 years, born Dec 1828 Ireland, parents born Ireland, immigration 1846
Johana Courtney, wife, age 36, married 44 years, 9 children, 4 living, born Mar 1836 Ireland, parents born Ireland, immigration 1836
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1900 United States Federal Census
Home in 1900: Florence, Oneida, New York, ED 15, Sheet 2A, Enumerated June 12, Dwelling 39, Family 39, Line 50 + Next Page, Sheet 2B, Lines 51-55
Residence : Florence Township (North & East Part), Oneida, New York
John H Courtney, head, age 42, married 14 years, born Dec 1857 New York, father born Ireland, mother born New York
Mary Courtney, wife, age 40, married 14 years, 6 children, 4 living, born Sept 1859 New York, parents born Ireland
Nellie Courtney, daughter, age 12, born June 1887 New York, parents born New York
Joseph A Courtney, son, age 9, born Jany 1891 New York, parents born New York
Humphry Courtney, son, age 5, born Jany 1895 New York, parents born New York
John F Courtney, son, age 2, born Feby 1898 New York, parents born New York