I haven't been to Boston in some time but these places were my "go-to's" and they all appear to be thriving still.
I always enjoyed checking out Hanover St. in the North End.
It's Beantown's version of "Little Itally" with plenty of loud guido types and big hair. They have everything from simple spaghetti houses, fine Italian dining and pastry. I would be almost certain that Parziale Bakery is still there. Definately worth checking out.http://boston.menupages.com/restaurants ... -cuisines/
I also used to like Durgan Park in Faneuil Hall. It's a loud, busy place that is a first class joint.
True Yankee fare that's simply prepared. They feature fresh seafood, big hunks of meat, Boston Baked Beans and clam "chowdah", arrogant service that's "playfully sassy" and some big communal dining areas.
It's considered kinda touristy to the locals and it's not exactly a place for a romantic dinner but I always thought it was pretty cool none the less. It's not real expensive either.http://www.arkrestaurants.com/durgin_park.html
If you're over in Cambridge, check out The East Coast Grill for some of The best BBQ in New England with lot's of fresh seafood both raw and grilled.http://eastcoastgrill.net/
Another tip, I HIGHLY recommend not trying to drive around Boston to get to where you want to go. It's very tough to navigate for the un-initiated as there are parts of town that have traffic patterns that make absolutley no sense to someone from a city where most of our steets are laid out in a simple grid and loop pattern. Besides, parking really sucks and and be quite the challenge. You can pretty much walk to most places, jump in a cab or take the "T" to wherever your heading from Beacon Hill.