The boat was heavily damaged by the fire and sank into the Hudson River at the Haverstraw Marina off Beach Road.
Sheriff's Office Chief William Barbera said when the man smelled smoke and opened the door to his sleeping quarters to investigate, the rush of oxygen caused a flash of flames, engulfing the victim.
The man's face and hands were severely burned, Barbera said. While his condition was not available, Barbera said the burns were not considered life-threatening.
An ambulance crew took the victim to the burn unit at the Westchester Medical Center in Valhalla. Barbera said the man was in his 40s.
Thiells Fire Department Chief Jason Parente said the boat was "fully involved" with fire when firefighters arrived on scene. Fire boats from Stony Point and Thiells pounded the craft with water, as other volunteers hooked up hose lines and watered down the boat and the dock area.
"We knocked the initial fire down to get it under control," Stony Point Assistant Fire Chief Nick Attolino said. "They tried to knock down the last bit but water got into the boat through holes," causing it to sink into the Hudson River.
Parente said some of the dock also was burned and two adjacent boats suffered heat damage,.
The fire was reported at 8:27 a.m., bringing out about 15 Thiells volunteer firefighters and additional volunteers from Stony Point. Officers from the Sheriff's Office and Haverstraw police also responded.
Barbera said the cause of the fire is being investigated.