Unfortunately none that I know of. You can check out Second Coming records near Harvard Square, they used to have a good metal selection. There used to be an amazing t-shirt place called Stairway to Heaven but they closed years ago
Yeah, Newbury Comics has a pretty decent metal selection - new releases are usually ultra-cheap, too. The one on Newbury Street also has a huge used section, so you might be able to find something cool there.
There is a new independent specialty shop for metal, punk, noise/industrial, etc. in Harvard Square. It's called Armageddon Record Shop and is an outgrowth of the original Providence store. www.armageddonshopboston.com (It's across the street from the 66 bus stop, next to iHop).