Authorities said both were recovered from the water and were rushed to Jamaica Hospital, where a 13-year-old was pronounced dead.
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Medics managed to get a pulse on the second teen, also 13, but he later died at the hospital, according to officials.
It happened in Spring Creek Park, near the North Channel Bridge.
The portion of the park is federal land, part of the Gateway National Recreational Area. Even so, the New York City Parks Department asks for people to swim safely.
"We are saddened to hear of this incident and urge everyone to swim safely," the department said in a statement. "Only swim in designated areas when lifeguards are on duty no matter where you are."
The two teens were reported to have been on the rocks at 11:40 a.m. when they disappeared. Witnesses said a group of teens were playing on a surfboard.
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"Two of them wasn't there. When the three came out, two of them wasn't there," said witness Isri Persaud.
Jamaica Bay is notoriously rough, officials say, and firefighters reportedly helped several others in the group back to shore.
Neither of the teens could swim.
"When the tides go out, there's a strong current in the channel," said witness Deven Dooboi, "The water sometimes it circles around and it can suck anything."
One firefighter sustained a minor injury in the rescue operation.
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No criminality suspected.
The investigation is active and ongoing.
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