Investigators sought a possible plotter in the United States.
Ridership on the subway was running at about normal levels for a holiday weekend. Columbus Day, a federal holiday, will be celebrated on Monday.
Throughout the city, stepped-up security that began on Thursday continued, with armed troops patrolling transit hubs including Penn Station, Grand Central Terminal and the Port Authority bus station.
Asked on Fox News Sunday whether a suspected plotter had made it into the country, New York City Police Commissioner Ray Kelly said: "That's certainly part of the investigation, yes".
Members of the city's elite Atlas anti-terrorism unit were set to sweep and ride subways bringing thousands of fans to Yankee Stadium in the Bronx where the baseball team faced possible playoff elimination on Sunday night.
Uniformed police officers were in evidence at smaller subway stations in neighbourhoods outside Manhattan, occasionally stopping riders to check backpacks or packages.
Police officials said reports of suspicious packages had more than doubled in the past few days, with more than 200 such calls since early Friday. No dangerous items have been found.
Police officers are on patrol in
New York City subway stations
Kelly said New York would remain on heightened alert until US intelligence authorities in Iraq could pin down the credibility of the threat. Increased subway security would be in force again on Monday, Kelly told CNN, and the situation would be monitored hourly.
Carol Charest, who was visiting from Massachusetts with several family members, said they were initially hesitant about riding the subway but ended up doing just that "and it was fine." She added that the police presence was reassuring.
Credibility of threat
Kelly and Mayor Michael Bloomberg have differed with federal officials over the credibility of the threat, which was based on an uncorroborated claim to Iraqi authorities that prompted raids by US and Iraqi forces and resulted in two suspects being taken into custody in Iraq.
A third was being sought, and The New York Times reported that he had been detained in Iraq.
The federal bulletin noted that authorities "have doubts about the credibility of the threat" but passed it along "to provide increased awareness out of an abundance of caution".
Mayor Mike Bloomberg said the
subway is under threat (file)
Kelly told CNN that the source on the threat had a track record of providing both reliable and false information. But Bloomberg said he had become increasingly convinced over the past few days that the threat was real and that he preferred to err on the side of caution.
"If you waited to make sure all of your information was accurate, you'd only find out after the event had taken place," he told WNBC television on Sunday. The mayor, who is facing re-election next month, continued over the weekend to urge New Yorkers and visitors to "go about our business."
One subway rider who gave his name as Billy took Bloomberg's message to heart, saying he was unconcerned. "I'm more worried about the Yankees," he said.
Another rider dismissed the possible threat, saying police were "all over the place" as she rushed through a turnstile.