NEW YORK — A large fire under a bridge sent billowing smoke over New York and shut down commuter rail service between Manhattan and the northern suburbs for over two hours on Monday. Television footage showed wooden pilings on a pier in the Harlem River began burning under the 138th Street lift bridge and FDNY marine units hitting the fire with water. Huge orange flames were visible, and plumes of white and black smoke wafted over the river and East Harlem. "The flames were really huge and it was really pitch black," said Jesus Ramos, a bank worker who saw the blaze as he came into the city from White Plains, N.Y. "It was a big giant cloud. It was really going way up to the sky, it was covering up everything." The fire began shortly before noon and was declared under control around 1:30 p.m. Metro-North — which, next to the Long Island Rail Road, has more passengers than any commuter rail service in the country — resumed service around 2:30 p.m., with scattered delays of up to 15 minutes. It said two of the four tracks on the bridge had been restored. The railroad was assessing damage on the remaining tracks and its impact, if any, on the evening rush-hour. Riders were instructed to use subway connections during the Metro-North shutdown. "I'm taking a cab with that lady right there," said Robin Klein, who came into the city for a doctor's appointment from the suburbs in Westchester County. "I don't know, people have to get home. This place is going to be insane in two hours," Klein said of Grand Central Terminal. The cause of the fire was not immediately known. Suburban commuters have had a tough go of it recently. The Long Island Rail Road suffered a week of service disruptions following an Aug. 23 fire in Jamaica, Queens, that damaged a switching system. On Thursday evening, a storm left downed trees on the tracks, causing LIRR suspensions.