M.S. stands for Methodist Episcopal, a denomination of Methodist that no longer exists. ME churches became part of the United Methodist Church.
Elmont and Valley Stream are in Nassau County, not part of New York City, but very close, on the Queens County border.
United Methodist Church website has a St John's at
2 Rottkamp St
Valley Stream, NY 11580
Valley Stream and Elmont are next to each other, possibly the cemetery or church was Elmont address at one time, or death cert is just wrong as to which village it is in.
If you pull up the above address on mapquest, you will see St. John's Cemetery down the road, about 6 blocks west of the church.
Only way to find out if this is it, is call, good luck.