Clayton is a town in Jefferson County, New York, USA. The population was 5,153 at the 2010 census. The town is named after John M. Clayton, a federal political leader from Delaware.The Town of Clayton contains a village named Clayton. Both town and village are northwest of Watertown.The Village of Clayton, nearby Cape Vincent, NY, and Alexandria Bay, NY are popular tourist destinations on the New York mainland side of the Thousand Islands region.