If you already have a rental car, I would probably just drive in. But I would park somewhere fairly central, and then just walk / use MUNI. Check out http://sanfrancisco.bestparking.com/ to compare parking lot prices. The cable cars are a fun (if a bit pricey) tourist attraction in their own right, and they are useful to travel among the attractions you mentioned.

If you do decided to use BART, make sure to get on at the Millbrae station, and not at SFO. It costs about $4 one way into the city, instead of about $8.