More than a dozen passengers were seen lying on dockside stretchers under blankets as they awaited medical attention on a chilly January morning.
Two people have been critically injured, the Associated Press reported.
The Seastreak Wall Street ferry hit the mooring as it docked about 08:45 after a trip from New Jersey.
The ferry, which was carrying about 340 passengers and five crew members, was able to dock and witnesses say people rushed to disembark.
Of 11 people with serious injuries, the most severe is believed to be a head trauma sustained by a passenger who fell down some stairs as a result of the crash, the Associated Press reported.
Pier 11 in Lower Manhattan has not closed as a result of the collision, avoiding a major disruption to water traffic.
The 140 ft (43 m) vessel remains afloat.
“We don’t know what happened,” a still-bleeding passenger told the New York Daily News.
“The boat hit something, and we went flying. People were bleeding all over the place.”
A woman who witnessed the crash from the dock told CBS News the boat did not appear to have been coming in at high speed, but said “it was a very hard hit”.
New York Mayor Michael Bloomberg has visited the scene of the crash, along with senior police, fire and emergency management officials.
Manhattan, an island, is served by several commuter ferry lines, the largest of which brings passengers from the Staten Island borough.
In 2003, 11 people were killed and dozens injured when a Staten Island ferry boat crashed into a pier on Staten Island, across New York Harbor from Manhattan. Dozens more were injured in a State Island ferry crash in 2010.
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