Detectives were led to him by a tip, after a combined reward of $24,000 was posted for information leading to his arrest.
He is being questioned by detectives. No charges were immediately filed.
A bus rider turned on the driver who denied him a free transfer Monday, stabbing him to death as passengers looked on in the first killing of an on-duty city bus driver in more than a quarter-century.
Edwin Thomas, 46, was driving the B-46 bus in Brooklyn when the attacker got on shortly after noon on Monday, police said. The man swiped an invalid fare card and sat down on the bus before asking for a transfer slip usually available to riders.
When Thomas told the man he didn't pay for the ride and couldn't get a transfer, the man punched the driver in the head and fatally stabbed him in the torso in front of other passengers, police said.
Thomas was rushed to a hospital where he was pronounced dead, and the attacker fled on foot. Police are offering a $12,000 reward for any information on the culprit.
Passenger Benjamin Stacking told television reporters that he heard the commotion.
"It's crazy because the bus driver was cool," Stacking said.
"He let me on. I was 50 cents short. He let me on and gave me a transfer. No reason to stab a bus driver if you are broke or have no money and can't get a transfer. No reason to stab a person."
Elliot Lee Sander, the Metropolitan Transportation Authority's executive director and chief executive, said Thomas was a seven-year veteran and characterized him as "a valued employee" who would "be sorely missed."
"Bus operator Thomas was killed while serving the people of New York City," Sander said. "This is an extraordinary tragedy for the city and the MTA."
Gov. David Paterson said in a statement he was "shocked and saddened" by the killing of Thomas, who the governor said "spent his career ensuring the safety of his passengers."
Mayor Michael Bloomberg described Thomas in a statement as a "good man who was good at his job of helping move New York City."
The mayor said he spoke with Thomas's son Jeffrey, offering the family his sympathies.
"In Edwin's memory, I ask all New Yorkers riding public transit tonight or tomorrow to take an extra moment to say 'Thank you' to our New York City Transit workers and I ask everyone to keep Edwin Thomas' family and loved ones in your prayers," the mayor's statement said.
The fatal attack on the bus driver, the mayor said, was "so shocking" partly because such violence has become rare. The last bus driver killed while on the job was Harvey Shield in 1981 in Brooklyn, the MTA said.
Assaulting an on-duty MTA employee is a felony.
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