I highly recommend Seven Grand (a sister to the place of the same name in downtown L.A.) and Polite Provisions. Sycamore Den is also good. It's been well over a year since I've been to Prohibition so I don't know if it's as good as it used to be or not.
So first thing I did when I joined was to see who else is here representing San Diego - not many of us. Found the old thread about San Diego bars to visit, and it hasn't been updated since 2011, so here's a reason to visit this fine city (other than beer, and sunshine, and great Mexican food...