But officials say it is too soon to tell whether they played any role in the morning rush-hour incident that injured at least 80 people.
Still, mechanical failure is being eyed in the crash.
Seastreak's chairman spoke to Eyewitness News exclusively Thursday afternoon outside the company's headquarters in Atlantic Highlands, New Jersey.
The company is asking injured passengers to contact the office for any help they might need. And there are some belongings here left behind in the chaos.
Barker says the NTSB has asked him not to discuss the investigation, but SeaStreak is fully cooperating. It is a family run business and this accident had hit the company hard in many ways.
In spite of the big gash in its right side, the Seastreak catamaran has been moved from the East River's Pier 11. It was taken to New Jersey, where the investigation will continue.
The city transportation commissioner says the ferry was coming in to dock at 10 to 12 knots, or about 12 miles per hour, when it collided with one slip and then hit a second.
Crash investigators from the National Transportation Safety Board and the Coast Guard were on scene to figure out what went wrong.
"We expect that we will be on scene about five to seven days, and again, that's the fact finding phase," the NTSB's Robert Sumwalt said.
The ferry only recently returned to service after being damaged during Hurricane Sandy.
"It was horrible," one passenger said. "There was blood everywhere. People were trying to help each other. We were taking the little rubber gloves and putting ice cubes in them and handing them to people. It was a horrible scene."
The NTSB will now examine the ferry's maintenance records, training records, propulsion and steering, and they will interview witnesses and the five crew members, who have already passed alcohol Breathalhyzer tests.
"There was a loud crash and the boat stopped instantly and everyone went flying," another passenger said. "A lot of people fell down the stairs. A lot of people go knocked down. I myself flew across the boat."
At his home in Red Bank, New Jersey, Wednesday night, ferry captain Jason Reimer said nothing about the crash. But the chairman of Seastreak, James Barker, was apologetic.
"We are simply shocked and stunned that this happened," he said.
Pier 11 has since reopened, with the focus of the investigation moving to New Jersey.
The Seastreak Wall Street has been in minor accidents before. Coast Guard records said the ferry hit a cluster of fender piles while docking in 2010, punching a small hole in the ship's skin. In 2009, it suffered another tear on the bow after another minor docking collision. No one was injured in either of those mishaps.
Such ferry accidents happen every few years in New York. In 2003, 11 people were killed when a Staten Island Ferry crashed into a pier on Staten Island after its pilot passed out at the wheel. Three people were badly hurt and about 40 were injured when the same ferry hit the same pier in 2010 because of a mechanical problem.
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