I commuted weekly for about 3 1/2 years for law school. Here are a couple of other options for you to check: (1) check with the extension office or Harvard housing to see if they have student rate deals set up with local hotels, (2) negotiate directly with the hotel yourself - you will be staying x nights during the course of the term - see if they will cut a deal, (3) Entertainment book, (4) second what someone else said, check student housing listings (or graduate student housing listings) when I went there were always students looking for someone to stay 1 night per week ($), (5) the housing office might have lists of community members looking for students to stay 1 night per week for extra cash.

Once you decide on whether you are going to train or fly, you need to start watching fares. Once the fare goes on sale, buy as many as you can (if you can lock in the whole term EXCELLENT).