When we went we stayed at 'Harding House' which is a really nice B&B in 'Cambridge' (near Harvard/MIT).
http://www.cambridgeinns.com/harding/
I think with the exchange rate at the time cost us about £500 for 6 nights, not sure what it would cost now.
The subway/underground is pretty good but once in the centre just walk around and there's a fair bit to see, it's an enjoyable walk just wandering along the freedom trail. My aunt took us on a 'Duck tour' on the last day and it was really good, I got to drive on the river! 😉