We were just there in June, of my birthday tour stops !
TJ was describing pier 39, if you go right down to the bottom you will see the sealions, and lovely shops on the walk down.
We stayed just a street of fisherman's wharf, and it was lovely for a stroll in the evening. During the day they have food stalls on the pavement and the chowder and fish filled rolls looked amazing, but hubby hates fish ! There is a bakery here to and you can do a tour or go in and have breakfast they sell their own bread and you can see it coming over head in baskets from the bakery, service was ok but you had to get your food at one end and your drinks at the other.
I really enjoyed Alcatraz, but you would be best to book in advance over the internet, they do an audio tour when you get there, one of the ex cons was there doing book signing so it was interesting to talk to him, the ferry goes from pier 27 I think.
When you walk towards golden gate bridge, from the wharf you will see the end of the cable star line, go early and get on the tram go up into sfo. Here if you look up hill, then right you will see the 'mall' area where they make the chocolate Ghirardelli, the factory is on the second floor, on the ground floor is just the ice-cream booth. My eyes were bigger than my belly in there !
We didn't get time to the wine country, but I drink White Zinfandel at home so maybe it was just as well.
I think when you go to any city, it's worthwhile just doing the open top bus tours to get your bearings.
Have a great time....take a coat it's colder than Ireland !!