Did I forget to mention that the "Shuttle" (Air service to NYC from Boston on either Delta or US Air) serves two of the worst airports in the US - Logan and Laguardia. It's always a hassle, and you're always delayed.

If you go, I recommend taking the train also. Even with GREAT plane shuttle deals...you still have to get from LaGuardia to Manhattan. Take a taxi each way and add $30-40 to the price of your ticket; you'll lose your cost advantage. Take the shuttle bus (ca. $20 RT) to downtown, and you'll probably have a fair amount of time waiting into and out of Manhattan...you lose any time advantage you might have had over the train. Train has the advantage also that you can often simply buy it at the station that day, so if the weather is crummy in New York on the day you decide to go, you can always decide NOT to go. Also, while planes have been cancelled on numerous occasions in my experience, trains are more often on-time in the Northeast and have never been out-and-out cancelled. With flying, you risk making your day trip a 2 day trip.

Driving sounds nightmarish to me. Maybe some people have done it, but given that you're entering new territory, you'll probably be stressed, harried and will be in a bad mood from the whole experience.

Personally though, I think spending that day exploring different areas of Beantown (or maybe checking out Providence) would be far more pleasant and enjoyable than a harried, expensive day (with 7-8 hours of travel time) in the Big Apple, even by your best choice IMO, the train.