The 140-foot boat had departed from Highlands, N.J., with 326 aboard and was moving at 10 to 12 knots toward Pier 11 on the East River when it hit the pier's Slip D, then continued to hit Slip B, Janette Sadik-Khan, the city's transportation commissioner, said.
"It appears to have had a hard landing," Sadik-Khan said.
About 150 firefighters and paramedics responded, officials said.
Investigations were quickly announced by the National Transportation Safety board and the U.S. Coast Guard and by the city's fire, police and transportation departments.
City officials said one of the critically injured passengers fell down a staircase and hit his head.
The Seastreak Wall Street catamaran ferry banged into the dock as it arrived on Wednesday morning (local time), officials said.
Some of the injured were carried out strapped to flat-board stretchers, their heads and necks immobilized. Soon after the accident, about a dozen passengers on stretchers were spread out on the dock, surrounded by emergency workers and firefighters.
Jacqueline Wegner, of Highlands, N.J., who witnessed the accident from the pier, told Newsday that the seriousness of the accident soon became apparent.
When passengers began to emerge from the ferryboat. "There was lots of blood," Wegner said. "I saw a man with a broken hand ... This was really a surprise."
When the ferry hit the mooring, "I saw the gaping hole under the hull. The captain was yelling to get help," Wegner said. She estimated the hole was about 7 to 8 feet wide.
"It looked as though the boat was going down," Wegner said.
By 10 a.m. most of the hundreds of firefighters, onlookers and passengers had left the pier.
Seastreak, based in New Jersey, "provides daily year-round ferry services from Atlantic Highlands and Conners Highlands, N.J., to Pier 11 Wall Street, East 35th Street, and shuttle service to the World Financial Center," according to its website.