Hemant Lakhani, identified as a British arms dealer, was accused on Wednesday of providing material support to terrorists and illegal weapons dealing.
The second man, Moinuddeen Ahmed Hameed, faces charges of money-laundering in connection with the plot.
Officials said Lakhani was arrested in Newark on Tuesday after trying to sell a shoulder-fired surface-to-air missile to FBI informants posing as Islamists.
The informants claimed he wanted to shoot down a large commercial airliner.
Hameed was arrested in New York, as was a third man, Yehuda Abraham, who is due to appear in a US District Court in Manhattan.
The FBI used informants posing as members of a Somali Muslim group to set up the men.
British and Russian authorities were also involved in the year-long undercover operation.
Bin Ladin praise
Lahkani had expressed support for Usama bin Ladin, a law enforcement official said.
"He said bin Ladin did a good thing with September 11, and they (the informants and the arms dealer) talked about shooting down commercial airplanes to hurt the American economy," the official added.
In November 2002 two shoulder-launched missiles were fired at an Israeli passenger plane taking off from Mombasa, Kenya, but did not hit the aircraft.
The Igla, the missile involved in the sting operation, is powerful enough to bring down a commercial airline.