Puy lentils in/near Brookline
You have to look hard, but they're there (I do think they were gone for a while, though)... in the dried fruit section, at the bottom, in pint containers. Not too expensive, either ($2.99 for a pint). I miss them in bulk, but pints are better than nothing.
When I need them in bulk and don't mind a nice drive out of the city, I go to Debra's Natural Gourmet in West Concord. Reasonably priced and you can get as much as you need (their bulk section is one of the best I've seen around here).
Also, I'm told by a relative that the "new" Whole Foods in West Medford still has them in bulk.