I am a Realtor with access to both MLS in Sonoma (BAREIS) and San Diego (SANDICOR). I am also familiar with both markets since I used to live in Sonoma County.
The actual City of Sonoma is a wonderful place to live. The city is peaceful, safe, and there is still that small town feel. If you are thinking purely investment I would personally recommend other cities in that county like Santa Rosa, Petaluma, Windsor... etc. These cities are served by US Highway 101 (4-6 lanes), while Sonoma is accessed by some two lane state highways. The area is great for retirement but other than the wineries and tourism there isn't the diversity of industry to drive development.
I love the San Diego climate, we get many temperate sunny days without the high humidity you experience down in Florida. If you prefer the ocean and beaches to miles of vineyards then I would definitely choose San Diego. Downtown San Diego (all of San Diego) are recovering very well and most prices I see are going up but like most major cities you are getting very little space for a lot of money. I don't know if your son will live in the property or it will just be a rental in 5 years but you should take into account high HOA fees, possible building litigation, and other factors that might narrow your buyer list in the future.
In summary, there is positives and negatives of both areas. Personally, the prices that you pay for a condo in downtown SD, I might buy a house instead. But that is only a personal opinion.