maller towns around wine country are a great option. They are quiet, have unique and amazing restaurants, there's plenty to do indoors and outdoors. You can do a day trip to the coast and visit an oyster farm and eat fresh oysters right from the water, visit small mom n pop type wineries or go to larger wineries with great tours, caves, and food. It's also not too far into San Francisco if you do want to have a night in a big city. Or visit smaller towns like Sausalito or hike through the redwood trees Muir Woods. Fall (Sep and Oct) are the best times of year up there in my opinion, especially in San Francisco
If money isn't an issue, check out The Carneros Inn. Friend from Chicago just stayed there and was blown away. The cottages are very well apointed with their own private courtyard including an outdoor shower. I would avoid Napa and look more around the Sonoma area. Healdsburg, Geyserville, etc are great.
These areas may seem touristy (i.e. wine country) but don't get nearly the traffic that napa does. It's reflected in how you are treated at the wineries and restaurants as well. Slower pace and more personal.
Another great visit is Monterey or Carmel. Again it's sort of touristy but many of the people visiting are from the greater regional area so it's local tourists. Weather is great that time of year. Check out the Hyatt Carmel Highlands hotel. I've stayed there before and the views are amazing. Very secluded.