The body of a man believed to be in his 30s was discovered on Tuesday night during a maintenance inspection of British Airways flight 177 from London's Heathrow Airport, a spokesman for the Port Authority of New York and New Jersey said.
This is the second time in a week that a stowaway has been found dead in a wheel well.
On Christmas Eve, JFK airport maintenance crew found the body of a stowaway in a wheel well of an American Airlines flight that landed in New York from Montego Bay, Jamaica.
Port Authority, local law enforcement and the FBI are investigating a possible breach of airline security at a time when the United States is in a heightened state of alert over terror threats.
"Access to commercial aircraft is always a concern," said FBI spokesman Jim Margolin. "And obviously with inbound flights we're relying on security measures at airports that are not within the control of US law enforcement or aviation authorities."
Port Authority spokesman Tony Ciavolella said the dead man found aboard the British Airways flight was carrying Nigerian currency and was decomposed, leading to speculation he might have boarded the airliner days earlier.
The plane had been in Lagos, Nigeria, on 22 December according to British Airways. A British Airways spokesman said authorities were awaiting results of an autopsy of the unidentified man.
"They have to determine the cause of death and the length of time he was deceased so they can determine where this person stowed away," said spokesman John Lampl.
"Of course it is of concern. We have to focus on where the plane has been the last few days and finely tune where the obvious breach of security took place."