The incident happened about a mile off Jones Beach just before 6:00 p.m. on Saturday.
Investigators say one of the men, 37, was tossed from the back of his 23' Trophy boat while on a fishing trip in the Atlantic Ocean.
Another passenger, 32, jumped in after him.
The operator of the boat, 36-year-old Anthony Marmo, apparently did not realize the two men went overboard until the boat was far enough away that they were out of his sight.
He called police for help.
Lifeguards from Jones Beach saw the two men and rescued them with a rowboat.
They were taken to Nassau County Medical Center for observation.
Marmo was arrested and charged with boating while intoxicated.
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