According to the Beer Advocate magazine Russian River Brewery, of Santa Rosa, makes the top two American brews. They placed seven of their beers in the top 100 beers of the world. Also on the list are two beers from the Bear Republic in Healdsburg and one from the North Coast Brewery in Fort Bragg (just to the north in Mendocino County).
The Russian River Brewery is considered one of the best in the country. Ratebeer.com lists it as the sixth best brewery in the world.
Most lists of top breweries in the country also contain Lagunitas. Their IPA is the top-selling IPA in California. They offer tours and tastings daily if you're in the neighborhood.