Why not go to all three? If you are just looking for one though, they are all quite different. Seattle is really nice if you're into music\art\culture related stuff, but I couldn't imagine spending 3-4 months there. There isn't that much to do, and the stereotype is true - it does rain
a lot. Especially from October on. You will be soaked, all the time. If you like hiking, mountain biking, rock climbing, rain forests, rivers etc., there is lots of wilderness in a very short drive. Once the Americans drive you insane, you can get to British Columbia in Canada within 3 or 4 hours - it's much nicer anyway.
I've only been to San Francisco a few times and haven't spent much time there, but I remember it being quite fun. I would imagine there would be a lot to do, and it's in California, so the weather would be great over that time period. The weather wouldn't be as nice as San Diego, but close. There is a
a lot of touristy stuff in San Francisco, so if you're looking for that, it would be the place to go.
San Diego is also great. It's extremely warm, has great beaches, and is within driving distance of Mexico, Los Angeles and the Joshua Tree National Park (my favourtie place in California).
Overall it would be an extremely hard choice. I'd recommend Seattle or San Diego though.