I have loved Book Trader for years! They are a wonderful New Haven fixture - a great independent bookstore with a veg-friendly cafe. The big cafe room is made of windows, like eating in a greenhouse, and you're surrounded by books! On nice weather days, take advantage of one of New Haven's rare outdoor patios and people-watch on Chapel Street.
The menu has had 2 vegetarian sandwiches forever: Vonnegut's (roasted) Veggies, which could be vegan if you hold the brie; and the Tempesto, a quite nice tomato & mozz sandwich. They've recently added a vegan option, the Feast of Eden lentil-quinoa veggie burger, which I have not gotten to try but have high hopes for. The (non-vegan) brownies are also Amazingly good and as big as your palm. Homemade iced tea and OJ are good drink options.
Super cute cozy bookstore cafe, surrounded by books on a charming part of Chapel Street. A winner!
Cons: only a couple choices