I agree on the diesels - I formerly worked in a building directly above the tracks (450 West 33rd). There were times that the building engineers had to close the vents because of the odor, though I can't say for sure if it was idling locomotives, or some work going on at track level.
The locomotives that run on the Empire connection are on electric power leaving Penn until they reach the ventilated tunnel, when they switch to diesel (maybe at CP Empire). And the reverse heading to Penn.
David