You might consider renting a car for a few days to explore around New England and then take the train/fly down to New York, as a one way rental can be quite pricey. If you do drive between cities, consider options other than the 95 corridor, as it's not a very attractive road for most of its length and the drivers are only a small step down from psychotic in places.

While actually in either BOS or NYC, a car is usually more trouble than its worth, as parking is rare and expensive and traffic often makes it faster to walk or take transit. Both are great cities, though very different in scale.