The alleged mastermind is a Moroccan Muslim born in Queens who has prior arrests for drugs.
He had enlisted a pal and planned to sell drugs in order to finance the purchase of weapons, law enforcement sources told the Daily News.
No specific synagogue had been targeted, and the plot was still in its early planning stages when detected by investigators with the help of an informant, the sources said.
Both men were caught on wiretaps discussing the plot, according to sources, who said the chilling plan had been hatched several months ago and appears to have pre-dated the killing of Osama Bin Laden.
Neither man has any known ties to terror organizations and no other arrests are imminent, the sources said.
The Manhattan district attorney's office is expected to hold a press conference later Thursday to detail the arrests.
In an unusual move, investigators with the Joint Terrorism Task Force had declined to prosecute the case, saying the plan was more aspirational than operational, sources said.
The district attorney's office then picked up the case and is expected to charge the men under a state anti-terrorism law.
The charges come more than a year after an Al Qaeda-trained terrorist failed in his attempt to bomb Times Square on May 1, 2010.
Faisal Shahzad, a naturalized Pakistani living in Connecticut, pleaded guilty to plotting to kill hundreds of New Yorkers with a bomb-laden SUV in the Crossroads of the World.
Law enforcement authorities have been on alert in the wake of the killing of Bin Laden for any retaliatory attack from the terror network.
The Yemeni wing of Al Qaeda has promised to avenge the death of the terror leader.
NEW YORK (CBSNewYork) – Less than two weeks after the death of Osama bin Laden, authorities captured a pair of alleged terrorists plotting an attack within the five boroughs.
There were conflicting reports Thursday about the two men now under arrest. They are reportedly homegrown, of North African descent, but that's not yet clear.
FBI officials confirmed they were not handling this case, and sources told CBS 2 it will be prosecuted by the Manhattan D.A.'s office under New York State's terrorism law.
Details of the plot are still sketchy, but Mayor Michael Bloomberg and Police Commissioner Ray Kelly are planning a 2:30 p.m. news conference to clear things up.
One suspect had apparently talked about selling drugs to raise money to buy weapons. WCBS 880′s Paul Murnane reporters they allegedly wanted to attack synagogues. 1010 WINS' Juliet Papa reported the arrests were apparently the result of a sting operation.
It's not yet clear if the alleged plot was more aspirational than operational.
Meanwhile, analysts scouring Osama Bin Laden's personal diary said it's clear the dead al Qaeda leader was committed to influencing others to attack America.
"He didn't want to let up on the big events. He wanted to do things that would kill as many people that he killed on 9/11. But he also wanted to inspire people who would think about individual terrorist activity," said security expert Robert Strang.
It's unclear what may have motivated the two newly arrested suspects, but so-called "lone wolf" terrorists with no official terror group affiliation remain a primary concern for both local and federal law enforcement.