The incident took place around 3:30 a.m. on the double-decker pier, which opened in December of 2011 as part of the city's $167 million East River Waterfront project.
The 45-year-old victim was sexually assaulted and then thrown over the balcony of the top level of the pier, which hangs about 25 to 30 feet over a glass pavilion and an outdoor seating area.
She suffered a fractured pelvis and a broken femur and was taken to Bellevue Hospital in serious condition, according to cops.
Police said it is possible that the victim knew her attacker, although it was not immediately clear how.
The suspect is described as a man in his 50s, about 5-foot-8 and 230 pounds, with dreadlocks.
The lower level of the pier is open from 6 a.m. to midnight, and the upper level is open from 8 a.m. to dusk. The structure doesn't offer any attractions, save for a hot dog vendor and multiple seating areas.
Elma Moore, 55, of Canarsie, often takes in the sun on Pier 15 during her lunch hour and after work. She said she works nearby on Maiden Lane and visits the pier once a week.
"In the evenings, I come up here, and I've never seen anything unusual," Moore said. "But I have never been here late at night, so I really wouldn't know what the security is like."
"It's very sad," she added.
Abdul, 56, who declined to give his last name, sells T-shirts on a stand almost every day until 6 p.m. on the outskirts of the Seaport.
"Yesterday I came and I saw the cops. I didn't even know what happened," Abdul said.
"We're supposed to help each other. This is New York; we're not supposed to hurt each other, but some people are animals," he added. "This is no good. Why do you have to hurt somebody?"