Sonoma much better if...
...you wind up in a room that faces the pool/courtyard area. There are a few rooms that actually face the outer parking lot in a building not attached to the main building. The property is nice and the rooms are better than Napa, even if you don't wind up in a cottage. All rooms have a fireplace. The town of Sonoma can actually be walked to and biking in the area seems pretty do-able.
Napa is crazy crowded compared to Sonoma. Go to Sonoma. The on-site restaurant is also very tasty. The spa is also good (and clean) - I always get a pedicure at Raindance Spa when I am in the area, even if I am not staying at the hotel.