I ll take this from your direction - going eastbound.From Newark Airport to the Secaucus Transfer you re above ground.From the Secaucus Transfer for a few miles, you re above ground, then you ll enter a tunnel under the Hudson River.Upon clearing that tunnel, and entering NYC, you won t be ground level; you re below; however you ll see a little bit of daylight-you ll be around 33rd St. - then you ll hit the Penn Station tunnel underground.
The first part of your trip is above or at ground level, as you pass over the Jersey Meadows. Then the train goes underground, through a long tunnel under the Hudson River. On the Manhattan side, the track is depressed below street level. At first you ll be (briefly) in sunshine, and then the track goes underneath the old Main Post Office, and then underneath Penn Station, where the NJT tracks end.
Not entirely. NJ Transit train run underground from Penn Station to just east of Secaucus Junction. Form Secaucus Junction onward, the train runs at or above ground level.Good luck
Both. Parts are under ground, parts are above ground, and part is in the tunnel.