Saidakhmetov is a Brooklyn resident and citizen of Kazakhstan. Juraboev and Habibov are residents of Brooklyn and citizens of Uzbekistan.
They are charged with attempt and conspiracy to provide material support to a terrorist organization. If convicted, each faces a maximum sentence of 15 years in prison.
More than 20 people have been arrested in the U.S. in the last year for trying to travel to Syria to join ISIL or other groups, including six Bosnian-Americans indicted earlier this month.
Habibov appeared in federal court in Jacksonville, Florida, and was appointed a public defender. It was unclear if the two other men had attorneys who could comment on the charges. They were scheduled to appear in federal court in Brooklyn later Wednesday.
Federal prosecutors say Juraboev first came to the attention of law enforcement in August, when he posted on an Uzbek-language website that propagates ISIL ideology.
"Greetings! We too want to pledge our allegiance and commit ourselves while not present there," he wrote, according to federal authorities. "Is it possible to commit ourselves as dedicated martyrs anyway while here?"
Officials said they believed he planned to travel from Turkey to Syria to join the group. Prosecutors say Saidakhmetov also threatened an attack in the U.S. if he was unable to join ISIL. Juraboev's plans included attacks against Obama or planting a bomb on Coney Island, officials said.
"The flow of foreign fighters to Syria represents an evolving threat to our country and to our allies," said state U.S. Attorney Loretta Lynch, who is Obama's choice to be U.S. attorney general.
Federal officials say Juraboev identified Saidakhmetov as a friend and co-worker with a shared ideology. The two exchanged messages on how to get overseas, and Saidakhmetov and an informant watched videos of ISIL training camps in Syria, according to court papers.
Habibov operates kiosks that repair phones and sell kitchenware in malls in Jacksonville, Florida; Savannah, Georgia; and Philadelphia. He employed Saidakhmetov last fall and winter and said he would help fund his travel, though he did not mention a specific sum of money, prosecutors said. The two were spotted in Brooklyn purchasing a ticket for Saidakhmetov to travel to Turkey, officials said.
ISIL largely consists of Sunni Muslims from Iraq and Syria but has also drawn fighters from across the Muslim world and Europe.
More than 12,000 foreigners are believed by intelligence services to have traveled from across the planet to fight in groups in Syria and Iraq. The volunteers come from at least 81 countries — around one quarter of them reportedly hold Western citizenship.
Al Jazeera and the Associated Press