The fishing vessel, the 74-foot Carolina Queen, ran aground just off Rockaway Beach and Beach 59th Street.
It was not known why the ship ran aground. It was listing several yards off the shore.
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Seven fishing boat crew members are accounted for and uninjured. They were plucked individually from the boat using a Coast Guard helicopter and a basket.
According to the New York City Office of Emergency Management, the New York City Police and Fire departments remain on the scene assisting the Coast Guard vessel.
A 25-foot Coast Guard vessel sent to assist the ship ended up overturning in the waters off East Rockaway Inlet.
The Coast Guard boat:
Five Coast Guard members were able to get to the beach uninjured and they are being treated. They were wearing protective gear at the time their vessel overturned.