The person in charge of a ship or boat is the skipper. Another word for the skipper is the "captain," but skipper is so much more fun to say.
Skipper is an informal name for the captain, a way to address the person who's at the helm of a boat or in command of a Navy ship. The word skipper comes from the Dutch schipper, from schip, or "ship." Sometimes this word is also used for the captain of a team or the pilot of an airplane.