Authorities said the men also plotted to shoot down a military plane.
James Cromitie, 55; David Williams, 28; Onta Williams, 32; and Laguerre Payen, all of Newburgh, were charged with conspiracy to use weapons of mass destruction within the United States and conspiracy to acquire and use anti-aircraft missiles.
All the suspects except Payen appeared in federal court in White Plains on Thursday, their hands shackled to their waists. Payen was expected to appear in court later Thursday.
Lawyers for the defendants, all of whom are U.S. citizens, did not seek bail.
In arguing against bail, Assistant U.S. Attorney Eric Snyder told the judge "it's hard to envision a more chilling plot" and described the men as "extremely violent."
They were "disappointed...that the best target (the World Trade Center) was hit already," he said, adding that the men were "eager to bring death to Jews." He also said Cromitie wanted to see what he did on TV and be able to say, "I'm the one who did that."
Earlier, Police Commissioner Raymond Kelly spoke at a news conference outside the Riverdale Jewish Center in the Bronx.
"They stated that they wanted to commit jihad," Kelly said. "They were disturbed about what happened in Afghanistan and Pakistan, that Muslims were being killed."
Kelly said he believed the men knew each other through prison. They had long rap sheets for charges including drug possession and assault. During the hearing Cromitie told the judge he had used marijuana on Wednesday but was clear-headed enough to understand the proceedings.
An official told The Associated Press that three of the men are converts to Islam. The official spoke on condition of anonymity because the person was not authorized to discuss details of the investigation.
Payen, who officials said is of Haitian descent, occasionally attended a Newburgh mosque. His statements on Islam often had to be corrected, according to Assistant Imam Hamin Rashada, who met Payen through a program that helps prisoners re-enter society.
Acting U.S. Attorney Lev L. Dassin said the defendants planned to shoot Stinger surface-to-air guided missiles at planes at the Air National Guard base in Newburgh, about 70 miles north of New York City.
The FBI and other agencies monitored the men and provided an inactive missile and inert C-4 to an informant for the defendants.
The confidential informant who broke the case told Cromitie that he was involved with Jaish-e-Mohammed, a Pakistani terrorist group. It is one of several militant groups suspected of having links to Pakistani intelligence. Jaish set up training camps in Afghanistan under the Taliban and several senior operatives were close to Osama bin Laden.
Cromitie expressed interest in joining the group to "do jihad," according to a criminal complaint.
According to state Department of Correctional Services records, Payen was released on parole in August 2005 after serving just more than a year in prison for attempted assault in Rockland County.
Onta Williams served just more than a year in state prison for attempted criminal possession of a controlled substance in Orange County. He was released on parole in August 2003.
Cromitie has been in prison at least three times under three different names, prison records show.
He served two years on a drug sale conviction and was released on parole in 1991. Then, under the name of David Anderson, he spent 2 1/2 years in prison for selling drugs in New York City before being paroled in 1996. Under the name James Crometie, he was convicted of selling drugs in a school zone in 2000 and spent almost four years in prison before being released on parole in 2004.
Mayor Michael Bloomberg and Kelly met privately with congregants inside the Riverdale Jewish Center Thursday.
Nancy Harris Rouemy said she was alarmed when she learned the news from a neighbor and definitely paused before dropping off her 4-year-old son at the Riverdale Jewish Center, where he goes to school. "However, the assurance is that the perpetrators were caught and my son wouldn't be in danger," she said.
"It is so upsetting," agreed her husband, Isaac. "If it was an actual bomb, it would be a disaster. It's not just a synagogue. It's a school and there are senior citizens who come here too."
The arrests came after a nearly yearlong undercover operation that began in Newburgh. The defendants bought a digital camera at Wal-Mart to take pictures of targets, they spoke in code, and they expressed their hatred of Jews on several occasions, according to a criminal complaint.
In June 2008, the informant, who was acting under law enforcement supervision, met Cromitie in Newburgh and Cromitie complained that his parents had lived in Afghanistan and he was upset about the war there and that many Muslim people were being killed in Afghanistan and Pakistan by U.S. military forces, officials said.
Cromitie also expressed an interest in doing "something to America," they said in the complaint.
In October 2008, the informant began meeting with the defendants at a Newburgh house equipped with concealed video and audio equipment, the complaint said.
Beginning in April 2009, the four men selected the synagogues they intended to hit, it said. They also conducted surveillance of military planes at the Air National Guard Base, it said.
Nihad Awad, national executive director of the Council on American-Islamic Relations, issued a statement praising law enforcers "for their efforts in helping to prevent any harm to either Jewish institutions or to our nation's military."
"We repeat the American Muslim community's repudiation of bias-motivated crimes and of anyone who would falsely claim religious justification for violent actions," the statement said.
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Associated Press writers Devlin Barrett in Washington, Michael Hill in Newburgh, N.Y., contributed to this report.
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