"This is a plot that would have involved martyrdom, explosives and certain of the tubes that connect New Jersey with Lower Manhattan," Mark Mershon, head of the FBI's New York office, said.
Mr Mershon said a year-long investigation had identified eight "principal players" in the conspiracy to bomb tunnels under the Hudson River used by PATH rapid transit trains that carry more than 215,000 commuters a day.
"We believe we intercepted this group early in the plotting and that in fact the plan has largely been disrupted," Mershon said.
The alleged mastermind, Assem Hammoud, a 31-year-old Lebanese national, was arrested and charged in Beirut.
Mr Mershon said two other suspects related to the plot had been arrested overseas but not yet charged.
He did not specify where the arrests were made, but added that six foreign governments were helping with the "ongoing" investigation.
None of the plot principals were believed to be in the United States.
According to Mr Mershon, Mr Hammoud had acknowledged being the plan's mastermind and a member of Al-Qaeda who had pledged his allegiance to Osama bin Laden.
The Lebanese security services would only say that the suspect had admitted under interrogation to belonging to an extremist organisation and preparing "a significant act of terrorism" targetting the New York transport network.
He was arrested on April 24 after a "long period" of surveillance that focused on his Internet use, they said.
Initial reports had identified the Holland Tunnel - the main road link under the Hudson River - as the principal target, but the FBI said the group had focused on the PATH tunnels that originate from the World Trade Centre site.
Mr Mershon said the plot had matured to the point where the group was preparing to carry out surveillance of the targets, establish a "regiment of attack" and acquire the necessary materials.
New York City has been on a heightened state of alert ever since the September 11, 2001 attack, and transport security was further ramped up in the wake of the 2005 bombings on the London transport system that marked their first anniversary yesterday.
Mr Mershon said the investigation had begun one year ago from an "intelligence standpoint" and evolved into a multi-national operation.