Whilst going to breweries is a lot fun don't rule out going to beer bars, the best of which have amazing selections of beer. In San Francisco Toronado, Monk's Kettle and City Beer (a small bottlO with beers on tap) are all well worth a visit as well as Beer Revolution in Oakland. As for breweries Russian River and Lagunitas are both sensational - for my money two of the best I've ever been to.
San Diego is a pain to get around if you don't have a car. It's big and spread out, there's not a lot of public transport and when I was there it was not uncommon for taxis to not show up. I'd much rather drink in Portland. As for breweries in SD, all the Pizza Ports are worth a look, Ballast Point (there location near hotel circle is a homebrew store/tasting room and Sculpin tastes great fresh), Alesmith is open on weekends and it's better than Green Flash, and Alpine Brewing are all worth a visit. Stone is a bit of a drive north and I found it to be a bit sterile. Not too far from Stone is Lost Abbey which is in an industrial area and it is a great place to visit. If you have time check out Churchill's, it's not too far from Lost Abbey - it's in an industrial ******** and it looks like a dump from the outside but it's a great pub. As for other beer bars in SD, Neighbourhood Bar in the cbd, Hamiltons and Toronado all have great beer selections.
If you have time spare a few days at least for Portland. For my money it's the best city in the USA for drinking beer. It's easy to get around, has good public trasnport (which is free depending on where you are) and has the highest density of craft breweries in the US (I think). You could spend two weeks in Portland alone drinking beer, it's that good. Deshutes, Hair of the Dog, Full Sail Brewing, Hopworks and Laurelwood are all well worth a visit. As for beer bars Bailey's Tap Room, Saraveza, Horse Brass and Belmont Station are all worth checking out as well. Shopping in Portland is good too because there is no state tax.
My number 1 recommendation for small brewpubs in the US has to be Walking Man, in Stevenson, Washington State. It's about a 45 minute drive out of Portland, which is very scenic, weather permitting. You would want to check the opening hours before you head out though, some days it's not open (maybe Monday and Tuesdays?) and when it is the hours may only be 4pm-9pm. There's 10 beers on tap, including my all time favourite Jay Walker. The beers are very good. The food is good too, any place that double fires their chips is quality.
