Henderson is a town in Jefferson County, New York, United States. The population was 1,360 at the 2010 census. The town is named after William Henderson, the original European-American land owner.The Town of Henderson is in the west part of the county and is southwest of Watertown. The Great Lakes Seaway Trail runs through the town along New York State Route 3 and includes a monument to its founder, William E. Tyson.