Míxquic, in the extreme southern part of Mexico City was a town swallowed up by the growing megalopolis. There is a beautiful Dya of the Dead celebration that's worth it even if it gets crowded with chilangos. Naolinco, Veracruz has a really particular celebration where you sing from door to door in exchange for food and alcohol, it's lots of fun! I'd consider those the two main options, both are fairly accessible and interesting, and also a lot of fun!

If you want to go really far off the tourist track, try Huaquechula, Puebla. It's a town outside Cholula that has an interesting, very syncretic celebration and the altars are semiotic banquet. But you can expect some weird stares, and it's not nearly as picturesque as the other two... PM me if you want more specific directions on how to get to any of these spots...