It happened at the Suntex Marina on Casseekey Island Road.
Johann Hoffend in Chopper 5 flew over the scene and said one of the damaged vessels was a yacht at least 30 feet in length.
He said there was a tremendous amount of smoke from the fire.
Palm Beach County Fire Rescue later said the fire damaged two vessels. It appeared they were a total loss from a photo of the scene.
No one was injured, fire rescue said.