The actor split from his third wife, Katie Holmes, last year. Holmes and their 6-year-old daughter Suri now live elsewhere in Manhattan.
"He just doesn't really need it anymore," a source told the magazine about the flat, which is located on the 10th floor of an East Village apartment building. "He's barely in the city ... . The only reason to keep it was when he had Suri and Katie and needed a real home in the city for them."
Cruise also owns mansions in Beverly Hills, Calif., and Telluride, Colo.