It's bad enough the TSA has made flying a chore. Now the airlines are making flying both a chore and an expense. I used to love to fly. Now, if the opportunity presents itself, I'd rather go by car.
So flying would still make sense, especially now that you can take Uber from the airport to mid-town Manhattan for a reasonable rate (as well as to Logan Airport from Boston).
Another alternative (gulp) is taking Amtrak. Even that is better than driving between New York and Boston.