After looking for your John R. Novak, I do not believe he is in the Baca books. Although I do find two possibles....
1, Johann Nowak,22, arr. June 4, 1881, with family of parents Joh. & Anna, and sibs Anna, Ludmilla, Agnes, Franz, Ludwig and Friediech, sailing on board the "Baltimore". Don't think this is your guy.
2. Johann Nowak, 23, arr. Sept 23, 1880, dest. Nebraska, with parents Franz and Johanna. Don't think this is your guy either.
I do believe this Johann Novak, age 24, arr. 1880, Baltimore is yours, from the Polish Arrivals at the Port of Baltimore by Jeanne Davis-White.
Also think that the John Noak on the 1880 census in Baltimore is yours, He is a shoe maker. Entered twice, first one on June 8 and second on June 10. He is with Vincent Forest and Joseph Benesch both times.
I didn't find anything for Mary in the Baca books.
Do you have a death certificate or obituary for John that would indicate an accurate place of birth?