Dont forget Boston Beer works.... you have to get a microbrew and some of the frenchfries (4 fries per spud)
For a little more upscale, try "Figs" on Newberry street and then walk to Armani Cafe for coffee and people watching (also on Newberry street)
Go to Copley square and just walk around. There are plenty of things to see and do (and eat) in a very small area. I never had a bad meal in little Italy... even the grocery stores have wood fired pizza ovens and sell by the slice.
A couple of other suggestions-- dont rent a car. Unless your doing side trips. Boston is the easiest town to get around on their Subway. Get a 'T-pass' (sold in 3,5,7 day passes) ride all you want. Cheap too. The subway is very, very safe (my wife used to ride from work at 11pm without worries)
If you can, get out to see the town of Salem... its worth half a day.
I could go on, and on. If you have any other questions, just PM me and I will rattle on, and on for you. Enjoy!
ATB,
-K