If you want to be located IN San Fran, I can't recommend, BUT, if you want to be between SF and Wine Country, try the city of Novato. It's just about half way between the two. There are a few hotels there. San Rafael is also nice, just a little closer to SF.
If you can, do the Wine Train - check it out. You can just ride it, or ride it to wineries and get off/on. Peju winery is very nice and has lovely vintages. There's also Francis Ford Copella's winery - more touristy, but kinda fun, and there's a shop across the street that has FANTASTIC olive oils, tapenades, and all kinds of great yummy things.
If you stay in Novato or San Rafael, you can drive to Larkspur and take the ferry into SF - it's a lovely trip and if you don't have to drive in the city, it'll probably be very relaxing for you.
I used to live in Novato and LOVED that area. feel free to contact me and I'll give you as much info as I can.
ENJOY!