The commuter rail really isn't bad. Make sure you know your train's schedule, and either buy a ticket in advance or have money with you.

While in Boston, the trains are fine (except maybe the orange line? Not sure what its status is right now), though they're generally packed (green line) and very noisy (red line). It's honestly easier to walk most places if it's close enough. Make sure you don't miss the last commuter rail train.

Oh, I don't know when they added these, but there are these kiosks where you can rent portable batteries to keep your phone charged. Saved my butt the last time I went into Boston