The discovery marks the second time in less than a week that a body has been found in the wheel well of a plane at the airport, CNN reported Wednesday.
The body was discovered while the aircraft's first officer was conducting a routine examination after the plane's arrival from London's Heathrow Airport.
The dead stowaway, a black male between the ages of 30 and 35, was wearing shoes and pants with some Nigerian currency in his pants pocket, the official said.
"The plane was in Lagos, Nigeria, on Christmas Eve, and we believe the man climbed into the wheel well while it was in Nigeria," he said.
The FBI, Port Authority, Queens district attorney's office and Transportation Security Administration are conducting a joint investigation, Ciavolella said.
On Christmas Day, the body of a man was found at JFK on an American Airlines flight from Jamaica.