After he left the Assembly, Thomas worked as a contractor for several years, but remained active in local politics. He was appointed Deputy Commissioner of Water Supply, Gas, and Electricity in January 1904, and shortly after being removed from the position in May he was appointed Collector of City Revenue and Superintendent of Markets. In 1906, he was appointed real estate appraiser for the Finance Department. In 1911, New York governor John Alden Dix appointed him Tax Commissioner of New York. In December 1915, Thomas was made under sheriff, a position he held for the remainder of his life. Thomas also served as a delegate to the 1912 and 1916 Democratic National Conventions.