Leavitt & Peirce has all kinds of stuff besides pipes and tobacco (old-fashioned grooming stuff, antiques, cuff links, etc.). It's a cool shop, but it probably depends a lot on random foot traffic from tourists visiting Harvard and it kind of reflects that to my mind. I didn't try their tobaccos, but they only have a few (mostly aromatics as far as I could tell).
Peretti is more of a serious pipe shop. Nice selection of pipes -- lots of high-end stuff, but also a really extensive selection of basket pipes and private label Peretti pipes. Amazing selection of tobaccos, many of them made or blended in the store. The staff and owner really know their stuff. It's everything a real pipe shop should be. I loved shopping there.
EDIT: I love burley, so I tried some of Peretti's burley blends (333, Boston's Best and Burley Slice), but others can recommend their English blends.