The evacuation comes after days of travel issues at the airport following last week's blizzard.
The Port Authority which manages the airport said breakdowns due to frozen equipment, baggage handling issues, staff shortages and heavier than normal passenger loads had caused problems in recent days.
On Saturday night US time, police were called in after fights broke out between passengers following flight cancellations.
Witnesses said passsengers from XL Airways France became angry after their flight was cancelled having already been stranded at JFK for more than two days.
Virgin Atlantic tweeted, "We are sharing a gate with another airline, and they have just cancelled there flight, causing the disturbance and the police being called".
The airport had closed on Thursday afternoon due to the storm and was reopened on Friday morning at 7am, causing a build-up of flights as the airport tried to clear the backlog.
Issues were further compounded when a plane turned back for an emergency landing after a false alarm, followed by a collision on the tarmac when a China Southern plane being towed at JFK clipped the right tail end of a Kuwait Airways plane.
Passengers were being advised to allow extra time and to call their carriers for specific flight information.
It is unclear when the waterlogged terminal will reopen.
