The accident happened inside the center tube of inbound tunnel just before 7:30 a.m.
The New York City Fire Department says the motorcycle rider was taken to Bellevue Hospital in critical condition. He was pinned underneath a bus and suffered a broken shoulder and broken femur.
In all, officials say 52 people suffered injuries. Fourteen people went to the hospital, but none of the injuries were considered serious.
Passengers on the bus were not seriously hurt, but were going to be checked out.
Buses and some cars began entering the south tube of the Lincoln Tunnel just after 8:00 a.m. Delays continued for hours. The center tube re-opened just after 1:00 p.m.
The accident also impacted bus commuters as service to/from Port Authority Bus Terminal was subject to hour long delays. Some buses were diverted to Secaucus Junction Rail.
NJ Transit trains cross-honored bus tickets to and from NY Penn Station Newark.
The accident remains under investigation.