A 31-year-old man was shot in the head and died at the scene. He was later identified as Omar Trent of Brooklyn.
Workers at the complex say the fight started on a three-level yacht docked there.
Police couldn't immediately say how many people were involved or what they were doing at the complex. Much of it closes at 9 p.m. on Fridays, though eateries and bars are open later.
Seaport managers didn't immediately return a telephone call.
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