Otaku Sekai in the Auburn mall, anime merch/gaming, they also have a lounge for movies, Japanese snacks, and books. You might see folks in cosplay.

That's Entertainment has a good sized manga selection, but they have their hands in every collectibles market, so space is their limiting factor- US comic books take up half of the space and the selection is fantastic. It's one of the coolest shops in Central Mass, if not THE coolest. It's a must visit.

Great Stories in Whitinsville has some anime/manga merch and some of the best prices on back issues. Great selection of newer comics, tons of games. I go here a lot, nicest people, clean store, well organized.

The Green Dragon in Rhode Island. Absolute gem. Worth the drive, especially this time of year.

Superworld Comics, out towards Holden. I've never been.

Crazy4Comics, in Northborough, mostly US comics, prices are hit or miss, not exactly organized. Big selection for a small shop. Expect to dig thru bins and stacks, then haggle. Very old school experience, geared towards the fervent collector that loves the hunt.

Hall of Comics in Westborough, the exact opposite of Crazy4Comics. Well organized, modern, good prices, friendly staff, almost exclusively filled with back issues. They have the largest selection of investment quality, graded/slabbed comics in the area. There's some legendary stuff in there. Like a museum but everything is for sale. Almost exclusively US comics- I don't remember seeing any manga.

Anime Zakka in Boston too, but it's a drive. I've never been.