My daughter is director of operations at Domaine Carneros, I visit every 6-8 weeks and was just there last week.
@DaveHuskiesFan had some good suggestions. There are great things to do in both valleys and you should be able to do both valleys in 3 days.
As stated above make reservations now. I can get you into Domaine Carneros but many of the wine rooms fill up even though they can cost $100 - $200 per person. Most are $50 - $100 and they wave the fee if you buy enough wine.
Persoanlly I think the best base to stay is Napa City. From Napa you can easily get to Napa Valley and also Sonoma Square is less than 20 minutes and Healdsberg is about an hour+ away - Calistoga is 30-45 minutes depending on traffic.
Adding to
@Dave's in Sonoma Square I'd consider the Edge Restaurant (part of Stony Edge WInery) - word is it will be getting a MIchelin Star shortly and on Thursday nights you can see Robert Kamen who wrote Karate Kid. Sunflower Cafe is a favorite as well for lunch or brunch - Girl and the fig is great as in La Soulatte. I really enjoy walking around the square and the Chocolate Cow or Sweet Scoops for ice cream is a nice topper.
Healdsberg is also fun to walk around and they have a hotel restaurant that has a wine wall where you can get some of the world's finest by the ounce - The Matthiason. I belong to the Journeyman sausage of the quarter club - amazing chacuterie.
In Napa Valley, as stated above Mustard's is a favorte, Charter Oak is great, Kenzo in Napa CIty - there are many many incredible restaurants - Yountville alone has Lucy, Bouchon, Bistro Jeanty not to mention the French Laundry. In Napa I like stopping at Model Bakery for a breakfast sandwich and Ritual coffee in the Ox Bow market neaxt door for breakfast or grabbing a croissant and coffee at Bouchon Bakery in Yountville. For lunch I order ahead at Gotts Roadside, Oakville grocery or the food truck at Clif Family winery (all between Oakville and St. Helena), then you can do an after lunch tasting nearby.
For wines I'd suggest FarNiente or Nickel & Nickel for big reds (either you can taste the same wines), Stony Hill for phenominal whites with a view of the Valley; Mayacamas - make the drive up Mt. Veeder - my favorite right now ; Pride at the top of Spring Mountain has great reds and whites. Bouchaine in Carneros would be a great one for both of you - they specialize in Pinots and whites. Trouchard is a small winery also in Carneros that has both Reds and whites and is very personal.
If you want to add beer to the visit - Russian River brew company in Windser and Mad Fritz in St. Helena both are great visits.
I can be overly enthusiastic - let me know if you want to have a private chat as I can add many many more or be very specific,, or if you can't get a reservation at Domaine Carneros!