The cause of the accident, which occurred around 8:45 am at Pier 11, at South Street and Gouverneur Lane, was not immediately clear, according to a spokesman for the New York Fire Department.
A massive gash in the ferry could be seen, and passengers, speaking on local television stations, described a huge jolt as the ferry pulled into the dock. At least 57 people were hurt, according to emergency officials, and a number of passengers were taken off the boat on flatboards with their heads and necks immobilized.
The ferry, operated by Sea Streak Ferry, provides daily service from Atlantic Highlands and Conners Highlands in New Jersey to Lower Manhattan, and can accommodate several hundred passengers.
The president of the ferry company, James R. Barker, told NBC News that there were 300 people on the ferry and that many of those who were injured were thrown from their seats.
One passenger, Chris Avore, speaking to ABC News, said the impact was similar to what one might feel in a car crash.
"Almost no one knew what was going on," he said.
The gash in the boat stretched several feet above the water line, and Barker told NBC that it struck a loading barge, which extends from the pier and is used for passengers to get on and off the vessel.
The ferry is 140 feet long and 30 feet wide. Photos provided by passengers to local news agencies showed shattered glass and other damage aboard the boat.
The city has been working to expand ferry service along New York City's waterways in recent years, and accidents are relatively rare.
One of the worst accidents in the city's history took place on October 15, 2003, when a Staten Island Ferry missed its dock and hit a maintenance pier at full speed, killing 11 people and injuring 70 others. A pilot, who had been incapacitated at the time of the crash, pleaded guilty to manslaughter, but investigators also faulted training and enforcement of safety rules.
Passengers said that as the ferry approached Manhattan Wednesday morning, it seemed like a typical morning commute, with some passengers typing on their smartphones, others reading a newspaper and some trying to catch a few last minutes of sleep.
But when it reached the dock, they reported a sudden jolt, powerful enough to send people hurtling through the air.
Even as paramedics tended to the wounded, some of those who were injured took to social media to describe what happened.
"I was on the ferry," Stephanie Agresta posted on her Facebook page. "Flew 10 feet. It was awful. Knee is messed up. Heading to hospital. So many worse. Send prayers."