The collections listed here cover California history on a broad scale. Primary sources held by the California State Library, for example, can provide excellent context for local Napa Valley history questions. Researchers will have some luck finding material about Napa Valley-related research questions in these larger collections as well.
Try searching your terms combined with place name keywords like "Napa Valley" or "Calistoga," or try searching for people and place names in general to see what primary sources are held by libraries, archives, and museums located outside Napa County. Because these searches comb through such large collections, you may need to sift through your results a little more, but the effort is worth the reward to see a photograph, letter, or digitized diary you might otherwise never find because it is located 500 miles away.