In Sonoma, I recommend Cafe La Haye, which is just off the square, LaSalette, which is on 1st St., and El Dorado Kitchen, which is in the El Dorado Hotel.
El Dorado Kitchen is QUITE good but may be a little out of your price range with wines etc.
For something different we really love a Taste of the Himalayas - (in a courtyard near Murphy's Pub if you like pub grub)
it's nepalese/indian food with emphasis on fresh tandoori dishes and breads. We have been there and met ex-Sherpas, Indian expats, business people and many locals who just like the food. It's tiny and very casual and if you go more than once you'll be treated like family. (their web address is not correct but i know it's still there)
We spent two nights in the Town of Sonoma. Our first night we ate ate the Red Grape. A very nice Pizza place. we enjoyed it . Good salad. Good Pizza.
The menu said " New Haven Style."
Second night was one of our live it up nights out. We ate at The Girl and the Fig. Good dinner. Flat Iron Steak for me, looked like New York Strip, Big Pork Chop for Mrs. With dessert and a glass of wine each , bill was about $100. Entrees were about $24 each.
The Lodge at Sonoma was a nice place to stay. About a mile from the town square. Some weekends , it looks like you can get a low price on priceline.
I ate at The Girl and the Fig last weekend and you will be hard pressed to beat that at least once. Atmosphere, service, wine list, and menu all in the same place.
That said, the square and immediate vicinity are filled with places that look very good to amazing. A wander and a try will likely bear very good fruit.
The food is great and staff friendly. The wine and beer selection is also very good. The experienced chef owner works the kitchen. The place is located among many vineyards so it a great lunch or dinner spot if you are out wine tasting. Make sure you have sticky toffee pudding for desert.