Waterstone's isn't indepedent. It's part of a large chain, which (IIRC, subject to correction) is UK-based.
If you're traveling outside Boston, consider Willow Books on 2A/119 in Acton and Baker Books on Rte. 6 in North Dartmouth (midway between New Bedford and Fall River). Baker has a nice home-grown software package for bookstores that Mac fans might find interesting. (Owner Ben Baker is religious on the subject of operating systems - I'm not justifying the attitude, just reporting it.)