Abdurasul Hasanovich Juraboev, 24, Akhror Saidakhmetov, 19, and Abror Habibov, 30, each face a maximum sentence of 15 years in prison if convicted.
Saidakhmetov, a citizen of Kazakhstan, was arrested early Wednesday morning at the John F Kennedy International Airport, where he was attempting to board a flight to Istanbul.
Juraboev, a citizen of Uzbekistan, had previously purchased a plane ticket to travel from New York to Istanbul and was scheduled to leave the US next month.
Habibov, also an Uzbek, had helped fund Saidakhmetov’s efforts to join ISIS.
Juraboev first came to the attention of law enforcement in August 2014 after he had threatened to kill President Barack Obama if ordered to do so by ISIS in a posting on an Uzbek-language website that propagates ISIS’s ideology.
The investigation subsequently revealed that Juraboev and Saidakhmetov devised a plan to travel to Turkey and then to Syria for the purpose of waging jihad on behalf of the ISIS.
In the posting, Juraboev said he wanted to "pledge... allegiance" to ISIS even though he was in the US and not in Iraq or Syria.
"I am in USA now but we don't have any arms. But is it possible to commit ourselves as dedicated martyrs anyway while here? What I'm saying is, to shoot Obama and then get shot ourselves, will it do? That will strike fear in the hearts of infidels," he said in the post.
According to the complaint, Juraboev was also prepared to engage in an act of terrorism in the US if ordered to do so by ISIS, and Saidakhmetov had intended to carry out a terror attack if he had been unable to travel abroad to join ISIS.
More recently, Saidakhmetov expressed his intent to buy a machine gun and shoot police officers and FBI agents if thwarted in his plan to join ISIS in Syria.
"The flow of foreign fighters to Syria represents an evolving threat to our country and to our allies," US Attorney for the Eastern District of New York Loretta Lynch said.
"We will vigorously prosecute those who attempt to travel to Syria to wage violent jihad on behalf of ISIL and those who support them. Anyone who threatens our citizens and our allies, here or abroad, will face the full force of American justice," Lynch said in a statement.
Assistant Director-in-Charge in FBI's New York Field Office Diego Rodriguez said the trio violated the true tenants of their faith in pursuit of their radical, violent agenda.
"We rely on help from the community, the public, and religious leaders to be mindful of those who could be radicalised. We cannot do this alone," Rodriguez said.