In addition to dedicated board game cafes, there are a lot of bars where people will bring their own games in Seattle. I've included a mix of formal cafes and bars where people often game.
Philadelphia has a few cafes downtown that are fun for gaming. Both have full kitchens in addition to board games meaning you can stay for hours!
Boston doesn't have a ton of traditional board game cafes unfortunately. Knight moves used to have a second location but it has closed.
Several big game developers are actually based in Minneapolis (or just outside the city).
There are board game shops all over the Bay Area! Here are a few of my favorites that I've been to.