The Helen Parker, a 31-foot tugboat, sank in the Hudson River at around 4:30pm.
The boat had picked up two people from Pier 90 at 50th Street and dropped them off on a construction barge off shore.
The 43-year-old captain was about to pull away from the barge when the boat tipped over.
He fell into the river, but was able to swim to the barge and was pulled out by the two people he had just dropped off.
The boat floated south down the river to around 41st Street where it sank.
The captain is being treated at a local hospital for minor injuries.
The Army Corps of Engineers has a side scan sonar on scene trying to find the tugboat.