St. Thomas Mar Thoma Church, New York church was formed in 1981 as one of the four parishes into which the Mar Thoma Congregation of Greater New York was divided. The new parish started with 63 families. The dedication service of the new parish was held at the Synod Hall on 110 Street and Amsterdam Avenue in Manhattan on January 25, 1981 and was led by the Episcopal Bishop of New York. Worship services continued at the Synod Hall from 1981 to 1990 by courtesy of the Episcopal Church. The church was incorporated under the Religious Corporations Law of New York in 1983. The church moved into newly purchased facility in Yonkers in March 1990. Presently the parish has a full time Vicar and about 220 families organized into ten prayer groups.
Seven parish organizations provide spiritual and support ministries to the members. The parish is a member of the Yonkers Council of Churches. The church Sunday School and Youth Organizations take part in suitable community outreach programs and local initiatives in the City of Yonkers.