We are visiting Boston for a month and wanted to find a grocery store that we could support. The Harvest Co-Op fits the bill as well as anything we were able to find in Santa Monica, CA. They are a CoOp with two locations (this is just for the JP location).
There was a great selection of fruits, veggies, and bulk grains and beans with a good sprinkling of vegan cookies and such throughout the store. They do have a deli section, but I would still call them vegan-friendly for carrying vegan substitutes and animal-cruelty-free soaps and other toiletries.
Cons: no parking lot, awkward checkout arrangement