Charles Ro Supply is owned by... Charles Ro who also owns the G-scale manufacturer USA Trains.
They generally cater to the O and G scale crowd, but they do carry HO, S, and N scales. (quite a bit actually)
They sell everything at a steep discount (25% or more off MSRP) because they order in bulk.
They're on Cross st in Malden. (beware, if you're heading up there from Boston, make sure that you're in Malden before you turn onto Cross st as theres a Cross st in Everett along the way!)
Hobby Bunker in Malden does the scale toy soldiers and tanks, etc. Great place to get HO scale Roco minitanks, although they do not sell trains.
Minutemen Hobbies in Braintree has a small selection of trains, but still good nonetheless.
South Shore Hobby in East Weymouth, MA is open once in a blue moon, but they do have dusty old boxes of stuff on their shelves if you're looking for anything that is out of production.
There really aren't any other hobby stores in the Boston area.
(Hobbytown in Quincy is out of business)