Some good information here. A few notes.
Fleet Week (usually the first week in October) is often the tail end of the little glorious weather we get in SF. September is usually great. June/July can be quite the experience for those not realizing what they are in for as it can be colder than it is in winter. Fog will move in after 2p with wind. Dress in layers!.
I think I might like the location around the Embarcadero (such as the Hotel Vitale mentioned) for a few reasons. It's not as touristy as the Fisherman's Wharf area where everyone eventually wants to end up, and the Ferry Building has a lot of nice food. You're not far away from the Wharf, walking distance to the great Exploratorium, and also close enough to the Union Square area. Bonus points for renting bikes, biking from the Embarcadero over the bridge and then taking the ferry back from Sausalito.
Highly recommend the Cal Academy of Sciences in GGP - outside of the Monterey Bay Aquarium, it's one of the nicest I've been to out here. The rest of the museum is nice as well, plus there are other things in the Park (bike rental, gardens, etc). Note that there's a great, and free, observatory on top of the de Young which is right by the Science museum.
15+ years out here and I've not gone to Muir Woods, mostly because it's super crowded and there are other options. But note that they now require reservations, and you must also take a shuttle in. From what I hear, you might want to book those tix now. : https://www.nps.gov/muwo/planyourvisit/index.htm
Old School Cal-Italian? Tadich Grill. Yet another reason to stay near the Embarcadero.
Depending on your boys, there's a few activities in the Crissy Field area which could be worthwhile
https://planetgranite.com/sf/hours-and-directions/
https://houseofair.com/
Combine those two with a short walk/exploration to Fort Point
I would recommend Alcatraz as well, though again you might want to think about booking now. Slots will definitely sell out during the summer months quickly.