The incident happened along the coast of Longport around 6:00 p.m.
Coast Guard officials say they were notified by New Jersey State Police that the charter vessel, Crystal Queen, was taken off the coast of Ocean City where it normally docks.
Officials managed to track down the boat and apprehend the man operating it.
He is being questioned by police.
The boat meanwhile is being towed to the Coast Guard station in Atlantic City to be processed.
There are no word yet on charges.