The official would not give further details about the charges the men face.
A second law enforcement official says the FBI was consulted about the case and declined to pursue it.
Both officials weren't authorized to speak about the matter publicly and spoke to the AP on condition of anonymity.
The New York Times and WNBC-TV report that the Manhattan District Attorney's Office plans to release further details about the men later Thursday.
New York City police have been on high alert for threats to the city since the U.S. raid that killed al-Qaida leader Osama bin Laden over a week ago.
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