here is the list of the 12 best cookies in san francisco from 7x7sf. i can only vouch for 2 on the list since that's all i've tried but i will recommend both the cookies & cream and gingersnap cookies listed.
9) Cookies and cream from Anthony's
Anthony Lucas' Mission shop switches up the cookie roster daily. But his regulars won't let him take away the cookies-and-cream flavor, specked with semi-pulverized Oreo chunks and perfect with a cold glass of Straus milk.