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Michael Appleton for The New York TimesJames Cromitie, one of the four men arrested on Wednesday night.

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Updated, May 21, 12:38 a.m. | Federal and city authorities arrested four men on Wednesday night on charges of plotting to bomb two synagogues in the Riverdale section of the Bronx and to use antiaircraft missiles to shoot down planes at a military base in Newburgh, N.Y., 60 miles north of New York City. (See a related article. See Thursday updates on City Room.)

The charges, which include conspiracy to use weapons of mass destruction in the United States and conspiracy to acquire and use antiaircraft missiles, represent some of the most significant allegations of domestic terrorism in some time. They come months into a new presidential administration, and asPresident Obama grapples with the question of how to handle detainees at theGuantánamo naval base in Cuba.

The four defendants — whom federal authorities identified as James Cromitie, David Williams, Onta Williams and Laguerre Payen, all of Newburgh, in Orange County — are to appear in Federal District Court in White Plains, in Westchester County, on Thursday morning. Three of the suspects are American citizens, and one suspect is of Haitian descent, according to the office of Gov. David A. Paterson.

Stan Honda/Agence France-Presse/Getty ImagesLev L. Dassin, the acting United States attorney for the Southern District of New York.

Mr. Cromitie, who is described as the lead defendant, is said to have told an F.B.I. informer that he had ties with Jaish-e-Muhammad, a jihadist group based in Pakistan. None of the defendants actually obtained weapons of mass destruction, according to the authorities. The men were, however, given an antiaircraft missile system that was incapable of being fired, as well as homemade bombs containing inert plastic explosives, as part of the undercover investigation, the authorities said.

Rabbi Jonathan I. Rosenblatt, the senior rabbi at the Riverdale Jewish Center, a modern Orthodox congregation in Riverdale, said the police informed him on Wednesday evening that his synagogue was a target of the plot, as well as the Riverdale Temple, a Reform synagogue that is a short distance away, on Independence Avenue. He said the police told him that the bombs were to have been detonated late Wednesday evening.

Rabbi Rosenblatt and several Jewish community leaders, including elected officials, were summoned to a meeting shortly after 9 p.m. Wednesday and told about the plot, he said in a phone interview. Rabbi Rosenblatt said he took the news with “shock, surprise — a sense of disbelief that something which is supposed to belong to the world of front pages and the evening news had invaded the quiet world of our synagogue.”

According to the criminal complaint, Mr. Cromitie met the informer last June, and told the informer that his parents had lived in Afghanistan and that he was upset about the deaths of Muslims at the hands of United States military forces in Afghanistan and Pakistan. Mr. Cromitie expressed interest in returning to Afghanistan and said that if he were to die a martyr he would go to paradise, according to the complaint, which states that Mr. Cromitie threatened to do “something to America.”

In July, according to the complaint, Mr. Cromitie and the informer discussed Jaish-e-Muhammad, and Mr. Cromitie claimed to be involved with the militant organization. Jaish-e-Muhammad was designated a foreign terrorist organization by the State Department in 2001.

That month, Mr. Cromitie also told the informer he wished to “do jihad,” the complaint states.

Starting in October, the informer began meeting Mr. Cromitie in a house in Newburgh that the F.B.I. had equipped with concealed video and audio equipment, according to the complaint. In several meetings at that house, Mr. Cromitie and the other defendants discussed their desire to attack a synagogue in Riverdale — a heavily Jewish neighborhood in the northwestern Bronx — and to shoot down military aircraft at the Air National Guard base in Newburgh.

Mr. Cromitie “asked the informant to supply surface-to-air guided missiles and explosives for the planned operations,” and the informer told Mr. Cromitie that he could provide him with C-4 plastic explosives, the complaint states.

Starting in April 2009, the complaint says, the four men selected the synagogues they intended to attack and conducted surveillance, including photographs, of military planes at the base.

Mr. Cromitie went to Riverdale, and, using a camera bought at a Wal-Mart, examined his targets, the complaint states. He “pointed to people walking on the street in the vicinity of a Jewish Community Center and said that if he had a gun, he would shoot each one in the head,” it states.

Later in April, Mr. Cromitie and David Williams bought a 9-millimeter semiautomatic pistol in Brooklyn to use in the planned attack, and then traveled to “a location from which they could shoot at the military planes using surface-to-air guided missiles,” the authorities said.

The two men indicated that they mainly intended to kill military personnel, but David Williams said if Jews were killed, “it does not matter,” according to the complaint.

In early May, Mr. Cromitie, David Williams and Mr. Payen drove with the informer toward Stamford, Conn., to obtain what the three men were told would be a surface-to-air guided missile system and three improvised explosive devices containing C-4 plastic explosive material.

The informer gave the men “a Stinger surface-to-air guided missile provided by the F.B.I. that was not capable of being fired,” as well as three improvised explosive devices, each containing more than 30 pounds of inert C-4 plastic explosives, telling the men that he had obtained them from Jaish-e-Muhammad, the authorities said.

The three men took the weapon materials back to Newburgh, and two days later, joined by Onta Williams, they met to inspect the materials and “further discuss the logistics of the operation,” the authorities said.

Lev L. Dassin, the acting United States attorney in Manhattan, said in a statement on Wednesday night that “the defendants wanted to engage in terrorist attacks.”

He added: “They selected targets and sought the weapons necessary to carry out their plans. Fortunately, the defendants sought the assistance of a witness cooperating with the government. While the weapons provided to the defendants by the cooperating witness were fake, the defendants thought they were absolutely real.”

Political leaders responded to the news of the arrests with statements expressing relief.

“While the bombs these terrorists attempted to plant tonight were — unbeknownst to them — fake, this latest attempt to attack our freedoms shows that the homeland security threats against New York City are sadly all too real and underscores why we must remain vigilant in our efforts to prevent terrorism,” Mayor Michael R. Bloomberg said in a statement.

Governor Paterson said in a statement: “Through the cooperation, hard work, and dedication of federal, state, and local law enforcement a serious threat was mitigated and terrorist attacks in our state were thwarted. Throughout the course of this investigation, law enforcement professionals have assured that all measures of security to protect our citizens were taken and, thanks to their watchful eye, at no time was anyone in danger.”

Senator Charles E. Schumer, Democrat of New York, said in a statement: “If there can be any good news from this terror scare it’s that this group was relatively unsophisticated, infiltrated early, and not connected to another terrorist group.”

Mr. Schumer added that he had spoken with the New York office of the F.B.I. and Police Commissioner Raymond W. Kelly, and said, “They have told me they have been monitoring this group for some time and that they did not have any connection to other terrorists.”