Cranes were used overnight to remove plane.
The Port Authority of New York and New Jersey said Friday morning that Runway 13 had not yet been reopened. The airport has two runways.
Six people were hurt in the incident Thursday. The nose of the plane came to rest just feet from icy Flushing Bay.
The plane was being taken to a hangar.
The National Transportation Safety Board plans to retrieve the flight data and cockpit voice recorders and to document damage to the aircraft.