I had read about this place on happycow and have come here twice, on both recent trips to San Francisco Mission District. Was just here in October 2012. Here's my Arizmendi Bakery review.
It's primarily a bakery that also makes pizzas, and it's and a great place to get a baked treat and a coffee in the daytime. I thoroughly enjoyed coming here, and if I lived in San Francisco, I would stop in everyday.
The coffee served at all the Arizmendi Bakeries in the Bay Area is Equinox brand and is good.
During both trips when I visited, there were several marked vegan items (1 vegan cookie, 1 vegan scone, 1 vegan muffin, 1 savory foccacia bread); plus you can find vegan-suitable bread.
Each day's pizza variety always contain dairy, so if you wish to have vegan pizza, you must custom order 24 hours+ in advance.