It always depends on your tastes, obviously, but bostnbill has hit some good points. In fact, I did not know where the cigar louges were at.!
If you're staying in the city, don't worry about where you are. It's safe, very small, and walkable from anywhere on a nice day.
food is great. The North End is where I usually eat. Many newer fish joints serve great seafood, and only get the New England Chowda' (the white kind).
In the fall, heh?
Taking in a Pats game?
tough ticket to get, but let me know. I'll take care of your tailgating supplies.