The trio, Abdurasul Juraboev, Abror Habibov and Akhror Saidakhmetov aged between 19 and 30, were arrested last month by the Federal Bureau of Investigation (FBI).
They caught the attention of the authorities, after they posted to Uzbek-language website in recent months.
The FBI said a suspect had pledged to kill U.S. President, Barack Obama.
Another allegedly tried to travel to Syria via Turkey in order to join IS, while the third was accused of helping to fund efforts to join the Syrian jihadist.
The three men appeared in New York’s Federal court on Friday, where they pleaded not guilty of the charges against them. After the session, the Judge had set their next court hearing for June 19.
The US has charged about 20 people with plans to join militant groups abroad, many who intend to go to Syria to fight for IS.
Figures suggest more than 20,000 foreigners have joined the fights in Iraq and Syria in the past three years.