On February 16, 2004, Thomas was traded to the New York Knicks in a three-team trade that also included the Atlanta Hawks. The trade also sent Keith Van Horn, whom Thomas was also traded for during the 1997 draft, from the Knicks to the Bucks, Nazr Mohammed from the Hawks to the Knicks, Joel Przybilla from the Bucks to the Hawks, and Michael Doleac from the Knicks to the Hawks.
