Thanks for the all the answers! Thing is, I'm still not sure I've understood - the question was probably a bit unclear:
NYP-BOS
Acela max speed: 150
Regional max speed: 125
Time difference b/w two: 20-25 minutes
NYP-WAS
Acela max speed: 135
Regional max speed: 125
Time difference b/w two: 40-45 minutes
The NYP-BOS is slightly, but not significantly longer than the NYP-WAS. Given the greater difference in top speeds in NYP-BOS, one would expect the time difference also to be greater in NYP-BOS. It's not, so my question was 'why?'
The why is because just because that top speed is 150 that does not mean that the train is cruising at that top speed for the duration of the trip. According to the '01 Timetable there are two segments totaling 18 miles (except for 2 curves on Track 1) that are rated for 150 MPH operation. 18 miles out of the 155 that Amtrak owns on the Boston-New Haven segment. Now the rest of the Speed for the majority of the run (not including curves and DSR's), 110, 125, 90, 85, 60, 85, 25, 40, 60, 70, 90, 95, 135, 65, 70, 135, 120, 110. Do the math. Now this does not include 56.5 miles of 90 MPH max running on Metro North, or the mere 3 miles of 100 MPH running on the Main Line from Harold to CP216.