How long are you in town for?
Things to see:
Fanuel Hall/Quincy Market - kinda touristy, but fun to see and has great nightlife.
North End - Great Italian food and if they have a festival all the better to walk around that area
Waterfront - usually fun to see the harbor
USS Constitution - Old Ironsides is a must see.
Rose Kennedy Greenway
Boston Commons
Fenway PAAHK!
Most of these places are in fairly close proximity and can be walked too.
Constitution is on one end of the city while Fenway Park is on the other.
B&M's
Cigar Masters - between Boston Common and Fenway - Great selection - they serve wine & beer w\ no Booze
Stanza Di Cigari - in the N End - Good selection high end is very pricey - $50 for Opus! serve all kinds of alchohol
Churchils - Just outside Fanual Hall (across the street) - Limited Selection - Wine & beer only
You will find at all these B&M's to be a little pricey due to the indoor smoking rules in Boston.
Churchills is a little more rundown but prices are OK.
Hope this helps.
Unfortunately Im booked for the week, or else I would offer to drive you around a bit.