Capt. Jason Roebuck said Tuesday morning that lifeguards and helicopters are still searching for the boy, but he expects the effort to end by noon.
Roebuck says Long Branch police are the last agency actively searching for the boy.
Family and friends reported the teen missing shortly before 5:45 p.m. Sunday. Police say friends told them he was swimming in waters off Pier Village when he went under and didn't come back up.
The Coast Guard suspended its search Monday morning after an approximately 14-hour search that covered 88 nautical square miles.
The boy hasn't been identified.