Edward Leary, 49, an unemployed computer operator from Scotch Plains, New Jersey, was charged with 45 counts. The bomb went off in his hands, Police Commissioner William Bratton said.
The bomb exploded Wednesday as the subway was stopped in a station, just one block east of the World Trade Center, where a terrorist bomb killed six people and injured 1,000 in February 1993.
Leary was under police guard at Cornell Medical Center, where he was in critical condition with burns to his face, knuckles and legs.
Leary became a suspect when he left the scene of the blast in lower Manhattan. He was found about two miles (three kilometers) away in the borough of Brooklyn, in pain and with his pants scorched and in tatters.
He was one of four passengers critically injured. Detectives questioned him overnight, and state and federal investigators along with New York City officers searched Leary's home in New Jersey and planned to return later Thursday to search further. Police were not talking about what they found. A residence in Brooklyn was also searched, Bratton said. Leary owns property in Brooklyn.
Bratton would not comment on a possible motive.
The explosion of the crude firebomb sent holiday shoppers into hysterics, inspired acts of heroism by passengers and triggered an emergency response that tied up downtown streets for hours.
Police said the bomb went off as the train sat with its doors open in the Fulton Street station, where an average of 50,000 people a day enter eight subway lines.
The bomb apparently consisted of a glass jar, a flammable liquid and a crude device that ignited the fluid, Bratton said. It was not clear if it went off accidentally or intentionally, he said.
An off-duty Transit Police officer, Denfield Otto, was on his way to choir practice at about 1:30 P.M. when he heard a series of popping noises. Fifteen seconds later, he said, there was an explosion and a wall of flames on his subway car.
"I got two people in flames, laying on the floor of the train," Otto said. "Some brave passengers took off their coats and tried to beat back the flames."
Otto raced to the station's token booth and came back with a fire extinguisher.
Officers Michael Ruiz and Anthony Roa were accompanying an ambulance taking Leary to the medical center when they heard a police radio broadcast describing a man seen leaving the subway after the fire.
"We said to each other, 'Hey, that sounds like our guy,'" Ruiz said. According to Ruiz, Leary claimed he walked through the subway tunnel under the East River after the fire.
Leary's neighbors said he moved to Scotch Plains with his wife and son a year or two ago. They said he recently lost his job on Wall Street, but his wife continued to work.
Governor-elect George Pataki issued a statement urging the death penalty for the person behind the firebombing.
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