The crash happened just before 9 a.m. between Dyer and 10th Avenues and West 39th and 40th streets.
The FDNY says at least 30 people suffered minor injuries.
Of those injured, 27 went to the hospital and three refused hospitalization. All of the injuries are said to be non-life-threatening.
Many passengers could be seen being carted on stretchers from the bus to awaiting ambulances with many wearing neck braces.
"A lot of them with musculoskeletal injuries, neck pain, back pain," said FDNY Deputy Assistant Chief Joseph Pataky.
The two New Jersey Transit buses made contact on the entrance ramp near the exit of the Lincoln Tunnel.
NJ Transit said the accident is under investigation but surveillance video clearly shows the bus in the rear zooming up the ramp and ramming the rear of the bus in front of it so hard that it physically pushed the bus forward.
The crash caused a log jam of buses, which added to the headache of the morning commute.
"I know that some of the traffic was able to operate based on other mean of entry of egress at the port, so it didn't impact us all together that much," said Port Authority Police Lt. Chris Howe.
The point of entry to the world's busiest bus terminal is being phased out. A new state-of-the-art terminal is planned for 2032 with new bus ramps connected directly from the Lincoln Tunnel.
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