I would suggest that you check out the rates at the Milenium Bostonian Hotel. It is across the street from Quincy Market, faneuil hall, and a 5 minute walf from the North End (little Italy).
Churchills is located in the Bostonian, and is one of 2 legal smokeing venues after May 5. How convenient for a cigar smoker.
It is also about a 2 minute walk govenment center where you can catch the "T" (public transit) to other parts of the city. Lots of galleries, restaurants and good shopping on Newbury St. Also visit cigar masters on boylston st (parallel to Newbury), the other legal cigar lounge.
The missus might enjoy shopping at filenes basement, but I suggest you stay away from there or it will cost you.
Try eating at Ida's ( my favorite restaurant in the North End) it's tiny and the food is great.
Enjoy
Steve