Thanks ya'll for your wonderful recommendations! We've added a few things on our schedule because of it!

I'm visiting again in November and twice next semester so there are other visits to catch everything. (though it might be too cold later on to do much)
Isabella Stewart Gardner House- a definate yes. It looks gorgeous. Too bad their classical music concerts at the museum line up with the days I'll be there.
We're probably going to have Legal Seafoods as a lunch destination rather than a dinner one.
We're definately going to walk along the Charles. I'm sure the weather will be lovely for it.
Probably going to check out Pizzaria Regina.
We'll have to catch Mike's Pastries next time- bf promised to take me to
Finale. Any of you been there?
Of course we'll visit Harvard square. The bf is in his last year at Harvard law school so it would be silly not to visit the square. hehe. He says there are bums there, but they're not violent so we can deal. lol.
I don't get to see him too often, so planning is essential!
I'm visiting Oct 8 - 12. wooohoo