For apartments or housing, look on PadMapper. If you like city living and the likes of it, and those things are important to you, stick with San Francisco. If you don't care, don't drink, don't do any of those things, startup life is better in the Valley but that's about all there is in the Valley (personal opinion of course). I live in the Valley (disclaimer).
That said, if you choose San Francisco, the city is small enough so that it doesn't matter where you are but if you want to be as close to the startup scene as possible, SOMA (district) is probably your best bet. If you want convenience, Richmond is close to a lot of food places that you can walk to on foot.
If you opt for the valley route, being as close as possible to University Ave in Palo Alto is probably what you're after.
