Besides the smoking issue, what type of area do you want to live in ? One with bars/restaurants, something quiet but easy access to the city, downtown feel ?

What location downtown are you working in (near which T Stop) ?

Depending on where you are commuting from might make the recommendation a little different. You don't want to be switching multiple subway lines to be commuting (you can, just a PITA).

You can live in the Longwood area out near the Fenway which is in Boston or something like Davis Sq in Somerville which will be busy and have a college/young sort of vibe. If you want quiet, then look at something more like Brookline maybe, still next to Boston.

Cheers.