If you have kids, they will love the Aquarium by the Bay.
You can walk underwater and there will be sharks swimming over you. At the end you can touch stingrays and other sea creatures. My wife touched an anemone and it stuck to her finger. This is a fun place and worth the money; if you bring a camera, make sure you have a fast lens—it gets dark in there.
You can buy a week-long city pass in San Francisco and for 60 dollars you get access to the museum, trolley rides, a boat trip that takes you under the Golden Gate Bridge, and more. We bought them for our whole family and had a blast going to all the museums and other things that were included. We loved our vacation to San Francisco and are planning another trip next year!