Roads leading to and surrounding the terminal were closed down as police investigated the threat.
Around an hour after passengers were ordered to leave the building they were allowed back inside as the all clear was given, according to Fox 5 New York.
Officers deemed the luggage to be safe, though it is not clear at this time why it was left unattended.
The security comes amid tension following the attack in Istanbul yesterday which left 41 dead and more than 200 injured.
The Port Authority of New York announced that additional armed officers were being added in high-visibility areas to reassure airline passengers in the wake of the terror attack in Turkey.
The FBI Joint Terrorism Task Force, along with local law enforcement, is coordinating security efforts with the agency.
All scheduled flights between the U.S. and Ataturk Airport, in Istanbul, were also suspended following the blasts, with ten inbound Turkish Airlines flights held briefly after landing in America.
Two planes arrived at JFK yesterday, with more flights arriving in Boston, Chicago, Atlanta, Miami, Washington and San Francisco later in the evening without incident.
Three men attacked Ataturk airport after pulling up in taxis, then shooting their way into the terminal building before detonating their suicide vests, police said.
CCTV images show desperate passengers fleeing for their lives as the bombs detonate, including one who blew himself up after being shot by a hero policeman.
The scenes of holidaymakers scrambling for the exits as explosions rip through the terminal sending ceiling tiles crashing down echo an almost identical attack in Brussels earlier this year.
The New York Port Authority had announced more armed security for JFK, La Guardia and Newark airports in the wake of the Istanbul attack, though added there is no specific threat against the city
Security experts in the U.S. have long warned about the problem of defending so-called ‘soft targets’, places where security is relatively lax but people still gather in large numbers.
Such attacks have been repeated over the last year to often devastating effect – from the attack on Paris last December, to the shooting at Pulse nightclub in Orlando earlier this month.
Speaking after the Paris attack, in which 130 people were killing in coordinated attacks on the Bataclan music venue, soccer stadium and cafes in the city center, John Kerry said: ‘Shopping malls, a restaurant — anywhere.
‘The idea is to make us believe that we are always going to be in such grave and imminent danger that we actually have to stop what we’re doing and change our choices and change our way of life.’
The attackers, who have yet to be identified, shot their way into the terminal at Ataturk (left) before detonating their suicide vests (right), sending passengers running for their lives
California Democrat Sen. Diane Feinstein, the ranking Democrat on the Senate Intelligence Committee, told NBC: ‘A building is one thing. It’s another thing to hit a soft target.
‘To walk into restaurants where people are having a Friday night dinner, to kill everybody you can kill. To go into a concert hall, do the same thing.’
The terror threat level in New York remains elevated following yesterday’s attack, meaning there is a ‘significant risk of terror attacks’, though officials said they are not aware of a specific threat against the city.