The Napa River, San Pablo Bay, and marshes in the Carneros offer calm, scenic spots ideal for paddleboarding and kayaking. You can rent equipment or book tours through Napa Valley Paddle, linked here.
October is an excellent time to take a hike. Trails of all difficulties are plentiful in the area. The Valentine Vista Trail in Moore Creek Park is a family favorite. Westwood Hills Park Loop is right in the middle of town and features an exceptional climbing tree for younger visitors. Please check out this website and the Land Trust of Napa Valley page for more ideas.
Early October is the busiest season for winemaking. Grapes are harvested, crushed, fermented, and transferred in to barrels to age all within the space of two (ish) months. This is a great time to see the process in action. This will mean that there will likely be more traffic in and around the valley. If you do wish to go wine tasting, be sure to book ahead. Also, do not plan to visit more than one or two wineries in a day. It's not fun to be in a rush.
When Molly was growing up, David Stevens made wine for Freemark Abbey, Chandon, and Bouchaine. Molly worked in Meadowcroft Wine's tasting room. Other favorites are Gloria Ferrer, Larson Family, Mumm, and Cuvaison (right around the corner from Molly's house!).
Hess Persson Estates on Mount Veeder not only hosts tastings and tours but also an impressive contemporary art collection. You can tour the museum for free and see works by Andy Goldsworthy, Francis Bacon, Katsura Funakoshi, Frank Stella, Gerhard Richter, and others. The drive up passes stands of Costal Redwood, another wonder.
Once, it was the furthest northern frontier town of Mexico, established to fend off Russian influence. The Bear Flag Revolt, a short insurrection which briefly made California an independent republic and later a state, took place there in the summer of 1846. General Joseph "Fighting Joe" Hooker lived there immediately before serving in the Civil War. Scream was filmed there.
Downtown Sonoma huddles around a pretty, european-style central square ringed by historic buildings. You can visit Mission San Francisco Solano, the Sonoma Barracks, a pre Gold Rush hotel, the villa of the last governor of Alta California (evocatively named Lachryma Montis), a really good cheese shop, and a store that only sells flags. Downtown Sonoma is about a 30 min drive from Downtown Napa. It is a good stop for families, history buffs, and gourmands.