A high-ranking law enforcement source, speaking on condition of anonymity, said investigators were probing what part prescription drugs might have played in the accident, which killed 10 passengers and injured 66 others, including three who lost limbs.
Early blood sample results from the pilot indicated alcohol was not a factor in the tragedy, the source said.
Investigators also were examining conflicting reports on the position of other crew members as the boat veered wildly off course, crashing into a maintenance pier hundreds of feet from the slip where it normally docks.
Witnesses said the boat did not appear to slow down as it approached the St. George Terminal on Staten Island on a windy Wednesday afternoon. The ferry was immediately moved to a nearby passenger slip, where rescue crews began their work.
Under city Department of Transportation procedures, the pilot and captain are typically both in the pilot house as the boat enters port. "If the policy ... was implemented at the time of the accident, we don't know," said Ellen Engleman, National Transportation Safety Board chairwoman.
The NTSB, which is leading the probe, began interviewing deckhands and engineering crewmembers Thursday, as well as survivors of the crash and their families.
Investigators were gathering background information on the crew and the pilot, Assistant Capt. Richard Smith, and were working to create a "72-hour history" leading up to the crash.
Smith, 55, remained hospitalized under police guard. Authorities said he bolted from the scene of the crash and twice attempted suicide at his home. He spoke with police Wednesday but was not interviewed in depth, Engleman said.
Investigators confirmed that Smith also was at the helm of the same ferry, the Andrew J. Barberi, when it crashed into the Staten Island dock in July 1995, injuring some passengers. That accident was blamed on a propeller failure.
The possible role of prescription drugs emerged in comments Thursday by City Councilman Michael McMahon, who represents northern Staten Island, after a briefing with city officials. He said Smith collapsed at the controls and appeared to have lost consciousness due to "health problems and medication" - reportedly for a blood pressure problem.
"By the time the other captain could get control of the ship, it was too late," McMahon said.
An attorney representing Smith, Alan Abramson, spoke with the pilot's wife Thursday.
"The family and all concerned hope that people will not rush to judgment," said Abramson, who had not yet met with his critically injured client. "Their prayers go out to all the victims."
Blood samples were also taken from the rest of the crew; some results were already in and under review, Engleman said. She was unsure when they would be released.
Engleman said the NTSB investigation would consider other possible causes, such as the weather and engineering factors, and could take up to a year.
Investigators were also speaking with an attorney for the ship's captain to arrange a session with him.
The hobbled ferry was moored next to the terminal where thousands of commuters boarded ships Thursday as service was restored. The ferry, with its free 25-minute cruise across New York Harbor, ordinarily carries 70,000 people daily between Staten Island and lower Manhattan.
The dead, one woman and nine men, ranged from age 25 to 52, police said. They hailed from all walks of life - an insurance lawyer, a diplomatic security expert at the United Nations, a chef at a Times Square hotel, an electrician.
Hospitals reported that three other victims suffered amputations. Eight people remained in critical condition.
In all, 66 people were treated for injuries sustained in the crash - 37 at Staten Island University Hospital, and 29 victims at St. Vincent's Hospital - including Smith.
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