Suggestions on where to stay in San Francisco?

My girlfriend and I are taking a trip to California the first weekend of April. We are staying the weekend in Sonoma and going to wineries. Monday we will be driving to San Francisco and staying there Monday and Tuesday night. The only two things we have planned for San Francisco is going to Alcatraz, and the aquarium thus far. Where would be the best place to stay? I would like a hotel that is close to things for us to do, but also would like a hotel with a great view of the bay. Any suggestions?? Thanks in advance!Suggestions on where to stay in San Francisco?
The hotel with the best views of the bay is Hotel Vitale. Located right on the Embarcadero with great transportatation and dinning options. You can catch the F trolly right outside the hotel. The trolly will take you to the piers where you can visit the aquarium and take the ferry to Alcatraz

http://www.hotelvitale.com



If you are renting a car return it when you get to the city. Parking in the city is expensive and public transportation is the way to go.Suggestions on where to stay in San Francisco?
I just got back from SFO. I go about three times a year, and have stayed at many hotels both downtown and by the airport. We just spent three nights at the Columbus Motor Inn on Columbus Ave.



It's three blocks to Fisherman's Wharf, and about three blocks away from the beginning of North Beach. The Inn has free parking, which is a big expense at other places.



Although the hotel only has three floors, the views were pretty good.