Agency spokesman J Peter Donald says the plane arrived at the New York City airport on Saturday. He says the money was in USD 100 bills.
The FBI is investigating whether the cash disappeared from the cargo hold in Zurich, Switzerland, where Flight 17 originated, or after it landed.
The airport's operator, the Port Authority of New York and New Jersey, says it cannot comment.
The airline says in an email that it could not confirm or comment due to the ongoing investigation. But it says it had "no indication that any valuables were removed from a Swiss International Air Lines aircraft" at JFK.