The incident happened just before 10 a.m. Thursday, near the end of rush hour, on the No. 7 train.
Eyewitnesses say he exposed and pleasured himself in public view as the train approached the Queensboro Plaza station.
Another rider snapped the photo.
The suspect is described as black male, about 6 feet tall and weighing about 180 pounds, last seen wearing a white shirt, blue jeans, black boots and sunglasses.
Anyone with information is asked to call Crime Stoppers at (800) 577-TIPS (8477).