Links to published records, and some histories, of various churches (primarily Reformed) that have been made available online. [$ = pay wall]
Baptismal and Marriage Registers of the Old Dutch Church of Kingston
Records of the Reformed Dutch Churches of Hackensack and Schraalenburgh
First Record Book of the Old Dutch Church of Sleepy Hollow, Now the First Reformed Church of Tarrytown (Yonkers Historical and Library Assoc., 1901) (Google e-Book), and at Ancestry.com $
First English Record Book of the Dutch Reformed Church in Sleepy Hollow (Tarrytown Historical Society, 1931) (Ancestry.com $)
Marriage Records of the Reformed Protestant Dutch Church of Schenectady, New York
Reformed Dutch Church of Kakiat, Rockland Co., New York, 1774-1864 (from the "First Church Book"). Published 1909.
Records of the Reformed Dutch Church of New Paltz
History of the Gilead Evangelical Lutheran Church, Centre Brunswick, New York
Records of the Gilead Evangelical Lutheran Church at Center Brunswick (no e-version available as of Jan 1, 2018)
Records of Christ Church Poughkeepsie, Dutchess County, New York, 1766-1916
Records of the Reformed Dutch Church of New Hackensack, Dutchess County, New York (Google e-book $). At HathiTrust (viewable, one page at a time download).
Reformed Dutch Church Clarkstown, Rockland County, New York (Ancestry.com $)
Records of the Dutch Reformed Church of Fishkill, Dutchess County, New York (Ancestry.com $)
Registers of the Births, Marriages and Deaths of the "Eglise Francois a la Nouvelle York" From 1688 to 1804 (Google Books $) [French Protestant Church of New York]