Unless you are going suburb-to-suburb, driving from the city of Boston to the city of New York is not recommended. The I-95 corridor is absolutely horrendous.
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.
Well, when I said, driving, I meant in general, not Boston to NYC, but you're right that driving in that scenario wouldn't make sense. I love AMTRAK, but service from Pittsburgh to anywhere is practically non-existent. Otherwise, it's a great way to see the USA rather than flying over it. But you have to have the time for leisurely travel.
A friend of mine who travels to New York frequently goes by Megabus. Fares are cheap and she says she has yet to run into the unsavory clientele which uses Greyhound.