The incident happened just before 5:30 p.m. on Virgin American flight 220 from San Francisco.
Eyewitness News obtained exclusive photos showing where the birds hit engine number 2. The pilot reported smelling smoke in the cockpit and declared an emergency.
Port Authority Police and the Aircraft Fire and Rescue unit responded.
The plane landed safely, and passengers got out with no injuries reported.
Authorities are inspecting the plane for damage.