The captain of the overloaded boat that capsized in New York Harbor, killing a mother and her baby daughter, could face federal charges as investigators examine whether he was running an illegal charter company.

Manuel Hernandez, 46, was transferred to federal custody on Sunday after receiving treatment at Brooklyn’s Maimonides Medical Center, sources told The Post.

Federal charges could be announced as soon as Monday.

Hernandez — whose last known address was a swanky condo building off Central Park South — had been facing 13 reckless endangerment charges after being taken into NYPD custody Saturday night, but these are no longer being pursued…

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