Assistant Captain Richard Smith was in charge of the helm when the ferry slammed at full speed into a Staten Island pier on October 15, 2003, killing 11 and causing horrific injuries as the side of the vessel was peeled open by pilings lining the dock.
Smith, who slashed his wrists after the incident in a failed suicide attempt, said he had passed out at the controls because of medication he was taking for high blood pressure.
Patrick Ryan, the city's former ferry director, was also sentenced to one year and one day in jail on related charges of negligence.
During the court hearing, families of the victims argued that the two defendants should receive the maximum possible sentences, with one comparing Smith to "a drunken driver."
Smith, who sighed deeply and looked grim during the relatives' testimony, offered an impassioned apology in a statement to the court.
"I will regret for the rest of my life that I did not call in sick that day," he said. "I was at the helm. I am responsible ... I failed in my responsibility to my passengers. I am truly, deeply sorry."
Some relatives said they appreciated Smith's words.
"I believe he is sorry for what happened," said Christine Santuro, whose sister died in the crash.
"He's the only one who stepped up to the plate and apologised," Ms Santuro said.
It was the worst accident in the Manhattan-Staten Island ferry service's 100-year history. A similar incident in 1995 injured 18, but no one died.
In passing sentence, Judge Edward Korman described Smith as a "broken man."
"Beyond whatever sentence I impose, he will suffer for what he did for the rest of his life," the judge said.