The plane took off from Westchester County Airport in White Plains and was headed to Fort Myers, Florida, when it hit the bird.
There were no signs of mechanical problems and no injuries were reported.
JetBlue says that in "an abundance of caution" the aircraft was diverted to nearby Kennedy Airport.
The plane landed safely at 8:25 a.m.
Passengers were put on another plane. They were expected to arrive in Florida about two hours late.
Federal transportation officials say nearly 10,000 aircraft collide with birds every year.
Bird strikes over New York have been getting special attention since 2009, when a flight successfully ditched in the Hudson River after hitting a flock of geese.