Larry's Comics at 66 Lakeview Ave is one spot with a good sized Manga collection.
Or try Tabletop Arena in downtown Lowell. They also sell comic books. These guys are really friendly and know a lot of people who are Anime fans, I'm sure this is the place to have meetups etc. They even had a cosplay event back in may.
Up to about 3/4 years ago, Barnes and Noble in downtown Lowell was my destination for purchasing manga, but UMass Lowell took over. I understand that there are free versions of manga/anime online, but like others, I'd like to support my favorites by buying their stuff. This is why we need an anime shop or hangout.
Another idea is to allow customers to pay by the minute/hour of reading multiple manga rather than paying $9+ for a single volume.