Thanks all ! I actually live like 5 in from LGA so for me getting to the airport is much quicker than getting into Manhattan and taking the train. I am going to have to be going to Boston pretty often now so I thought I would start off with the airline that was the best , but it seem that the consensus is that there isn't a ton of difference.
It is for business so they pay ground transport and the flight so cost isn't a huge issue.
Thanks very much for the informative and super helpful replies