The boat caught fire while docked at Pier 59, south of Chelsea Piers, just after 2:45 a.m.
Flames tore through the sailboat, the Quid Pro Quo, and spread to a power boat docked nearby.
The fire lit up the West Side sky before being put out by firefighters.
One man, believed to be the owner, who also lives on the boat, was injured.
The cause of the fire is under investigation.