Depending on where you're staying and when you're arriving, I'd suggest considering taking a taxi or public transport to a location outside the city of Boston (for example, one in Cambridge) and renting a car from a "neighborhood" office. Often the savings in taxes and fees alone will pay for the ride.

In particular, if you are staying over the weekend I'd check Enterprise again - their local offices usually have very good weekend rates and they might even pick you up from the airport.