Several FDNY vessels responded to the Futura Marina, located on Knapp Street in Sheepshead Bay, just before 4 p.m., authorities said.
Firefighters extinguished the fire and worked to keep the vessel afloat. The fire was under control just before 5 p.m., the FDNY said.
Video from SkyFOX showed that the charred vessels appeared severely damaged, possibly irreparably.
No one was hurt, the New York City Fire Department said.