I live about 30 minutes from BOS by bus/rail. Let's say everything is timed perfectly: I get TSA Precheck, 10 minute curb-to-gate, 5 minute wait, boarding commences at T-20, first in line for takeoff.

That means I leave for the airport 75 minutes before my flight, fly for 1 hour, arrive in JFK/LGA/EWR, and then take about 30-40 minutes of public transit to my destination in Manhattan. And that's the ideal.

There's some break-even point for travelers between the more relaxed pace of train travel as opposed to the efficiency of air travel, but BOS - NYC is still within the realm of the train, even at Amtrak speeds.