To my taste, the best burrito in SF can be found at La Corneta in Glen Park. I lean toward the super carne asada, but the fish (salmon) burrito is also amazing. The Glen Park La Corneta has amazing food in general and if you go there, you will not be disappointed.

Be advised that La Corneta also has a location in SoMa (on Mission) but the taste of the food is entirely different, not bad, but not as much to my liking.