The Delta flight was over Elmhurst around 8 p.m. when a green laser beam entered the cockpit twice, an FBI spokesman said.
The beam injured one of the two pilots, who experienced "flash blindness" and had a disruption in vision. He also continued to experience pain in his right eye after the flight, the FBI said.
FBI officials determined that the beam originated somewhere on Queens Boulevard.
“Laser incidents are often viewed as harmless," said George Venizelo, the FBI's Assistant Director-in-Charge.
"This couldn’t be further from the truth."
The incident is the most recent in New York City that has injured pilots preparing to land at local airports.
On Jan. 24, a laser beam that came from Staten Island injured a United Airlines pilot preparing to land at LaGuardia Airport.
And last December, a pilot had blurry vision for more than a week after he was temporarily blinded while preparing to land his JetBlue airplane at JFK Airport.
It's not clear where that beam originated.
The FBI's Joint Terrorism Task Force is leading an investigation into the three incidents, and anyone with information is asked to call 212-384-1000.
Callers can remain anonymous, and there is a $10,000 reward available for information that leads to an arrest.