Unless you're passing through Fisherman's Wharf, avoid it. Brutal tourist trap, it stinks, is way too crowded considering the junky stuff there is to do there, and is one of those places you'd almost never find an actual resident of the Bay Area.
A Giants game is an awesome time, so you've got that covered.
I assume you have a car? If not, I think you should get one. There is SO much to see outside of SF at a very short distance.
As far as eating goes:
Brown Sugar (Oakland/Across the bridge) - Breakfast, amazing, get the chicken and waffles
Noodle Theory (Berkley/Across the bridge) - Dinner, great noodle house
House of Nanking (Chinatown) - Chinese, if you walk down Post or Geary to Kearney, you can walk north to this spot (20 minutes maybe). The wait staff isn't great but it is some of the best Chinese you're ever going to eat. They'll also make you something special if you request it, but you don't control what that is and sometimes it's awful. You never know though!
La Taqueria (Mission) - One of the best burritos you'll ever have. We get off the plane and head straight there every single time.
Hog Island Oysters (Embarcadero OR road trip) - Great oyster spot if you like oysters, and if one of you don't then the other options are pretty great too.
Blue Bottle Coffee (Embarcadero OR Oakland) - great cup of coffee. Worth making a trip for (especially the iced coffee).
Possible things to do in SF:
Biking, do a lot of it to explore, or just walk!
Chinatown, you can walk to it.
Coit Tower, you can walk to it.
Union Square, it's a neat area to explore, get some Levi's (I think the flagship is around there).
Embarcadero, before or after your Giants game, you can walk from AT&T to Fisherman's Wharf in about an hour (stop at the Ferry Building along the way).
Baker Beach - Nice beach with some great views of the Golden Gate. Plus you can get naked on the north end of that's your thing.
Castro - Not a ton to do, but a hugely iconic spot for the gay rights movement. Worth exploring even if it's not a cause personal to you.
I would avoid Haight Ashbury, it's apparently nowhere near the counter-culture hub it used to be (it's touristy now).
Things to do outside of SF:
Oakland - try to go on the first Friday of the month, they have a huge block party on Main Street. A good mix of old Oakland of new Oakland. Lots of great spots to eat here too, just avoid walking around the sketchy places by yourself at night.
Berkley - good college town, some nice walks and shops. Drive up the Berkley Hills and you'll be treated to some of the most amazing views of the Bay you could ask for. Even if you don't stop in Berkley, make the time to go up the Berkley Hills. I promise you'll love it.
Point Bonita Lighthouse - Long drive off the highway, but it's a beautiful one and the end result is equally so. You can usually spot some whales from here depending on the season.
Highway 1 North - Take a drive up the coast and enjoy the views. Stop at Hog Island along the way and have some oysters (this is the better spot than the Embarcadero, but you shuck them yourself, I recommend bringing some picnic stuff).
Highway 1 South (Monterey) - The better drive of the two. Spend a day going down the highway and take it all in. Amazing drive. Head down to Big Sur and explore a little, and then turn back and stay in Monterey. Go to the aquarium. It's the best one I've ever been in, period. (You can also just go to the aquarium and back to SF in one day, but it's worth staying over).
Any questions, feel free to ask. These are just a few highlights.
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