Queens District Attorney Richard Brown said Friday that charges against 21-year-old Tamarcus Hines include gun possession and grand larceny.
A criminal complaint says on April 22 the Queens resident allegedly took the unloaded 9-milimeter gun from a locked box packed in the suitcase, along with ammunition and a gun holster.
The sergeant alerted authorities after arriving in Orlando, Florida.
Port Authority police say an investigation led to Hines. Detectives say Hines told them he had tossed the gun into a Queens sewer. The gun was later recovered from the sewer by police.
JFK International Airport is located on Long Island in Queens County, New York, about 12 miles from Lower Manhattan.