Novato is in Marin County and not a close or easy drive to either San Francisco or Wine Country altho' it might appear to be on a map. Are you planning to spend one day each in San Francisco, Napa and Sonoma--or 2 of the 3 in San Francisco? The latter is what I would strongly suggest doing since there's so much to see and do there. And this is one situation where changing lodging would be much more convenient than driving back and forth between locations. Your time is already quite limited. Stay 2 nights in San Francisco and one night in either Sonoma Town or Napa Valley (towns of Napa or Yountville would be good choices). If you must stay all 3 nights in one location, from San Francisco you could hook up with a tour group that will take you into both Napa and Sonoma Valleys for the day, or there's always the possibility driving yourself if that seems more attractive.Edited: 10:11 am, May 05, 2012
Staying in Novato would not be the first choice for most visitors. You will experience more of San Francisco, Napa, or Sonoma if you actually stay in them overnight. It's hard to enjoy the great restaurants in the City or Wine Country if you are staying in Novato.
However, if those things are of no interest to you and you just want to do day trips to each, then Novato is not a bad choice. It's just 30 minutes from the closest wineries in Napa and just 30 minutes from Healdsburg and the Point Reyes Visitor Center. It's also an easy half hour drive to the Golden Gate Bridge. If you do stay in Novato, you could take Golden Gate Transit into San Francisco and not have to bother with driving in the City and finding parking.
So, Novato is actually a great central location to stay in if looking for a good base and there are a few good restaurants there as well. Just be aware that it won't have the ambiance and excitement that staying in San Francisco or Napa would have.
If this is your first trip to the area, 3 days does not really give you enough time to cover both San Francisco and wine country. However, you could stay in San Francisco and take a day tour to wine country. There are a few tour companies that pick up/drop off in SF and tour Sonoma and/or Napa.
However, trying to do both in 3 days is doing justice to neither. And staying in Novato is not an efficient way of trying to see the area.