The incident occurred Sunday as JetBlue Flight 657 from Syracuse was flying at 5,000 feet over Long Island.
Published reports say the first officer suffered an eye injury and immediately notified the control tower. The plane landed safely.
The FBI and the FAA are investigating.
There were more than 3,500 aircraft laser incidents in 2011, compared to fewer than 300 in 2005.
The lasers are marketed as tools to point out stars at night. They are many times more powerful than the laser pointers typically used by lecturers.