I will be traveling from NY/NJ-Boston this summer and actually decided to fly instead of take the train. Why? A couple of factors:
Cost - it was more than $100 cheaper to fly than take the train, even factoring in the cost to get out to Newark. I booked pretty far in advance and was still shocked at the difference in price.
Travel time - even factoring in time to get to the airport, it’s faster to fly than it is to take the train, even before delays. Security is pretty quick using TSA pre-check, and hanging out in the lounge at Newark is infinitely preferred to the 7th circle of h-e-double-hockeys-sticks that is Penn Station.
Delays - when Amtrak works it is fine, but especially this summer delays have been BRUTAL, especially through NJ. Granted, NJT is worse but anything that messes up the tunnel (thank you Gov Christie) negatively impacts Amtrak as well.