Affordable towns for commuting to San Francisco *and* Napa?

Wow, i don't even know where to begin with your post. First off, before you commit to the huge cost of moving and uprooting a family, spend the time to actually come here, stay in a place like Petaluma (which is still sort of affordable) or Vallejo (which is affordable but will be a God awful commute for both) and then try to either drive (a must to work in Napa) or drive or take the bus/ferry combo into SF a few days during the morning and evening commutes. As a Mom who until recently worked, I can honestly say that having both parents doing those two crazy opposite drives is completely unsustainable. What happens when a child is sick at school & a parent has to pick them up? When you have to work late? When a car breaks down? At the very least you both would have to stagger your schedules so that 1 parent left the house at 4 or 5 am, and drove back in time to get home by 3 or 4 pm. The other parent would have to start late and work late. At best, you are looking at least at 2 hours commuting to/from SF daily- if there are accidents, mass transit problems, etc. it could be closer to 4 hours per day. Also, your combined transit costs are going to be high- either transit or driving/parking daily. On top of all of this, you have the high cost of housing- plan on spending around $3,000 per month on a 2 bd apt. in the boonies. And, for instance, the public schools are often terrible in the boonies (ahem, Vallejo.) If you both still really want to move to the Bay area, honestly, you need a more well thought out plan. The stress and high cost of living here is very real as the population grows and resources become more scarce and all forms of transportation become more difficult. I wish you luck in your journey, but you need to be realistic, if only for your kids' sake.

I would say your biggest concern should be your commutes. If I were in your position, one or both spouses should definitely try to get some flex arrangement so you don't have to be on site 5 days/week. The towns I would look at are Vallejo (the SF commuter takes the ferry, Napa drives), Benicia (driving to Napa, not so hot two-bridge commute to SF unless you drive to BART in Walnut Creek and take the train from there, or drive to ferry in Vallejo), or El Cerrito within walking distance of BART for the convenience of the SF commuter, 40ish minute drive for the Napa worker. Schools are hit and miss in Vallejo and Benicia (you can always go private) but you're okay in El Cerrito. Vallejo is the most affordable but does have its issues in parts. I would definitely rent for a while until you try out these commutes. Childcare is way cheaper in Vjo/Benicia than El Cerrito.

Lake Berryessa would be too far for you to commute to San Francisco. Benicia has good schools and is commutable easily to both San Francisco and Napa. There is a ferry in Vallejo that goes to San Francisco. Homes are relatively affordable for the bay area. If you are interested I can recommend a realtor for you to work with. I have been living in Benicia since 2001 and would be happy to answer any more questions you might have. 

Raising my hand to recommend Richmond in the East Bay, specifically my neighborhood, East Richmond Heights. We have a Bart stop (El Cerrito del Norte) into the city and a bridge (the Richmond-San Rafael Bridge) that goes straight up to Napa. In the nabe are loads of great elementary schools: Mira Vista is the public school, there is a cooperative elementary school called Crestmont, there is a Jewish day school called Tehiyah. And we are right on top of Wildcat Canyon. Technically, you could hike from there to Tilden Park in Oakland, though I've never done it; regardless, there are tons of great trails right here. Childcare is ... not cheap. When we finally got both kids into public school we wanted to take a bath in the money we suddenly were saving. Ah, bay area, you kooky place. 

My thought is with a child, one parent needs to be close enough to home, as to avoid a 3 hour commute home, which is what it will be from SF during rush hour.  And on Fridays in the summer, Ive seen it take 4 hours.  So my recommendation is not to cause both parents to risk a congested commute.  Someone needs to get home to the child in a reasonable time.  

Lake Berryessa is very affordable, but you can still find something small and affordable closer to town that is a short distance to the Vallefo Ferry.  Any safe neighborhood in Oakland will cost more anyway.  For SF, you can use BART but your husband will be in traffic getting out of the east bay and into Napa.  The drive from Napa to the Vallejo ferry is quick via a back way.  So do not consider driving to SF.  Ferry ride is only 1 hour and relaxing.  You can arrive home to your family in a sane condition.  Vallejo is also affordable and makes huge sense for commuting to both Napa and SF...but it is consistently rated an undesirable city due to crime.  Id actually consider Vallejo for myself, but not with a child.  

If youre set on having one take BART west and one drive east, Id recommend El Cerrito or Pinole for a smaller town feel and potential affordability.  El Cerrito has a great BART station with parking.  

I work in Napa and live in Berkeley.  Lake Beryessa is a real trek   Staying East of University is a big help with the commute (it's about an hour door to door-mostly against traffic).  I would look in Albany, El Cerrito and Berkeley.  You can bart in to SF and it keeps his commute doable. Nature is close by and the schools are good.  Good Luck!