A spokeswoman said the vehicle was "cleared without incident", NBC News reported.
Terminal B was evacuated around 11.30 p.m. on Thursday as police began looking into the car. It was later towed away and the terminal reopened.
The incident caused long delays for arriving and departing passengers.
Authorities imposed the lockdown after a person drove the car up to the terminal, jumped out and ran away.
Last month, two terminals at the John F. Kennedy Airport were evacuated after reports of gunfire which was later attributed to a large group cheering for Usain Bolt at the Olympic Games 2016.
New York remains tense after a bomb exploded in Chelsea on September 17, killing 29 persons.
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