I've been about 6 or 7 times (I'm good at finding excuses to go back), most recently 10 weeks pregnant in early October 2006, and exactly one year later with a 5 month old baby in tow. It might be a while now though.
San Francisco's climate is generally quite mild - less hot than other places in summer and early autumn, warmer than here in November and late February/early March. Actually, my visits there in Feb/March the weather's been a bit like it has on the nicer days here lately.
I love the city but have never got round to Alcatraz in 5 or 6 visits - we have various friends (mostly dp's originally) that we want to catch up with and my dream holiday is mostly secondhand bookshops, mooching in cafes, meeting up with friends and sucking in the atmosphere rather than tourist stuff.
I like the Mission district, Valencia's nicer to walk along than Mission Street.
Do you have any preference for cuisine? San Francisco is reputed to have the best Chinese food outside China, and we found a couple of favourites which we've returned to several times. You can eat out at very reasonable prices.
Mission, Noe Valley (more gentrified area near the Mission) and Haight Ashbury have some lovely new and secondhand bookshops, and record shops if that would appeal more to your teenage boys.
A ferry ride sounds like a good plan, Lombard Street and the cable cars, but re cable cars the queues can be enormous.
What do your sons most like doing when they're at home? That might help those of us who love SF to offer you advice. I don't suppose they have a particular interest in politics, 60s music and history, beat poetry or crime fiction or science fiction, just some of the things which influence what I like to do there.