Napa winery picks -
Castello di Amorosa - The wines are mediocre at best, but the castle is amazing.
Clos Pegase - The wines are nice, the staff is friendly, and the art around the estate is neat.
Frank Family Vineyards- These wines are excellent. The Zinfandel Port is amazing. The old stone winery is gorgeous.
Domaine Chandon- Reasonably priced and easy drinking sparkling wines, and the grounds and estate are very pretty.
Foodwise, your options are almost endless.
Definitely check out the CIA, Oxbow Market, Mustards Grill, Taylor’s Automatic Refresher, Oakville Grocery, Cindy’s Backstreet Kitchen, and Go Fish.
I second staying in Calistoga, it’s just such a nice little downtown. Dr. Wilkinson’s is a nice resort with motel-like rooms that are perfectly comfortable and clean, I spent my bachelorette party weekend there. Calistoga Inn is a little more plush, and the food and beer there is good as well.
If you like beer, then you are absolutely required to stop in Russian River Brewing here in Santa Rosa. Good pizza, outstanding beer.
If you aren’t set on Napa, there are tons of wineries in Sonoma County I can recommend. Some of my faves - Hartford Court, Merry Edwards, Dry Creek Vineyard, Lambert Bridge, BR Cohn (really good oils and vinegars too), Armida, and, well, I could go on and on here.
Good eats in Sonoma County - Hopmonk Tavern, Barley & Hops, River’s End, Dry Creek Kitchen, Flavor, Jack & Tony’s, and it’s a Bay Area chain - Mary’s Pizza Shack for pretty decent Italian food. Awesome meatballs.
Other things to do - The Charles M. Schulz museum is fun and interesting and the only museum I’ve ever become a member of. 
Armstrong Woods - Redwoods in Guerneville.
Next Wednesday is the first night of Wednesday Night Market in downtown Santa Rosa. Lots of food vendors and fruits and veggies.
Point Reyes - A nice drive out to the lighthouse, the town Point Reyes Station has lots of foodie adventures, including Cowgirl Creamery (they are also in the Ferry Building in SF, which should definitely be on your city to do list.) And one of the nicest B&Bs I’ve ever stayed in - One Mesa - Beautiful, comfortable, wonderful hosts, delicious breakfast.
Where to stay in SF - I also llike Hotel Triton, you really can’t go wrong with any of the Kimpton properties, the Personality Hotels properties, or the Joie de Vivre properties. The JdV properties are usually the cheapest of the bunch, and most are just as nice.