The San Diego Reader has produced a list of San Diego's top twelve breweries*. In the article, the breweries are listed in alphabetic order:
Alpine Beer Company
Amplified Ale Works
Ballast Point Brewery and Spirits
Green Flash Brewing Company
Monkey Paw Pub and Brewery
New English Brewing
Port Brewing / The Lost Abbey
"Best of" lists are fun, but frivolous. Sure, I read the articles touting the 100 greatest movies of all-time, or the ten best books of the year, or the top fifty beers to drink before you die, but there is bias and personal preference in any 'best of" list, which make them more opinion than fact. Some of my favorite movies are not going to show up on any "greatest" list, just like some of my favorite beers won't be on a "best of" list. I'm sure the publication of the supposed twelve best breweries in San Diego corresponds with San Diego Beer Week (SDBW). I would not argue against any of the breweries on the list, but there are plenty of good breweries in San Diego not on the list, so don't limit yourself to just a handful of breweries. SDBW is a great opportunity to sample the best from many different breweries.
* Brandon Hernandez who wrote the article for San Diego Reader also works for Stone Brewing, so Stone was excluded from the list.