The van went off the marina pier, at the end of Russell Street, in Howard Beach just before 8:30 a.m.
It landed on a large white boat, docked at the end of the marina.
The driver, who was rescued from the water by an NYPD Harbor unit, was taken to Jamaica Medical Center with non life-threatening injuries.
Police say the van driver was eastbound on the Belt Parkway when he sideswiped a Chevy Tahoe. The driver fled the crash scene into Howard Beach. He drove down a dead end street, crashed through a fence and landed on a boat.
The van was registered to an adult day care center in Queens. No passengers were believed to be on the van at the time.