There are several major differences between the two regions. Beginning with location, Sonoma borders the Pacific ocean along its western coast and in the southeastern edge of the wine region it borders the San Pablo bay. Sonoma and Napa are separated by a low lying mountain range and so Napa is due east. As such Napa is farther from the coastal weather influences, namely fog and cooler temperatures. As Napa's southern end also borders the San Pablo bay, this region is cooler due to the proximity to the water.
In general wine regions with more fog and cooler temperatures are best suited for thinner skinned grapes. Within Napa Valley as you head north and away from the bay, the temperature can increase from 5-15 degrees warmer. This makes it ideal for thicker skinned grapes. Sonoma as a wine region is famous for producing some astounding Pinot Noir, and Chardonnay. In areas of northeastern Sonoma farthest from the coast, there are many vineyards producing amazing Zinfandel and Cabernet Sauvignon.
Napa has a lot of climatic variation for a small region, however Cabernet Sauvignon is the king of Napa Valley. Overall Napa Valley is most famous for producing big bold full-bodied red wines. Another major difference is size. Sonoma is at least twice the size of Napa, while having half as many wineries. Sonoma wineries are, as a result, more spread out and, as a region, you will find more small cities and other forms of industry (it stands as one of the largest dairy producing regions within California).
The grape varietals grown in Sonoma include: Barbera, Cabernet Franc, Cabernet Sauvignon, Craignante, Chardonnay, Chenin blanc, Cinsault, Gamay noir, Gewurtztraminer, Grenache, Malbec, Merlot, Mourvèdre, Muscat, Cannelle, Petit Verdot, Petite Sirah, Pinot blanc, Pinot gris, Pinot Meunier, Pinot noir, Riesling, Roussane, Sangiovese, Sauvignon blanc, Sauvignon Musque, Sémillon, Syrah, Tempranillo, Tinta Cao, Tourliga Nacional, Viognier & Zinfandel.
While both wine regions respectively had wineries open dating back to the the 1850's there were several events that occurred in Napa that helped to further both wine regions. By the early 1900s there were roughly 200 wineries between both Sonoma and Napa wine regions. A major outbreak of vine disease called phylloxera followed by Prohibition and the Great Depression greatly impacted the regions wine industry and by the 1930s only a dozen or so wineries remained.
Robert Mondavi was an innovator and winemaker that helped to create the reputation of the Napa Valley in the 1960's as a region that focused on quality instead of quantity, and worked to make Napa one of the best wine regions in the world. This dream came to fruition in the 1976 Paris Tasting when Napa wines won against France, and thereafter Napa was seen as a region capable of producing some of the best wines in the world.
Napa's fame has brought tourism dating back to the late 1970's and early 80's while Sonoma has dates to beginning in the 1990's. Both regions offer gorgeous scenery. Sonoma with its vast rolling hills spotted with cows and sheep is a nice neighbor to Napa, a narrow wine valley, more densely planted out with an amazing assortment of grapevines.