557 Haight St, San Francisco, CA 94117
A few GF beers on tap
2400 Harrison Street, San Francisco, CA 94110
This caters more to veganism but there are definitely GF options. Similar to Gracias Madre though (which they own), if you're veganism isn't what you're really going for then you can get similar Mexican dishes at a cheaper price elsewhere. However, they do serve up pretty delicious looking quinoa bowls, who h you can't get at most places. Moreover, their shakes are awesome.
1062 Folsom Street, San Francisco, CA 94103
Pretty food GF pizza and delivery was fast. The price is a bit steep but for GF convenience, you can't beat it. I also have to watch for tomatoes and their white pizza with artichoke, spinach, and basil was just right. They indicate which brand crust they use so if you're so inclined, you could always order online and make yourself to avoid the costs of ordering out.
2211 Mission St, San Francisco, CA 94110
Their menu mainly caters to vegans but you can get some tasty GF items by ordering things with corn tortilla instead of flour. However, if you're looking for a meatier Mexican option you can get something cheaper and just as tasty at other Mission eateries since most serve corn tortillas.