Its really a personal decision.
If you like bigger cities, ability to see Pt. Lobos, Big Sur, aquairum, etc. choose Monterey Bay.
If you like small towns, wine tasting, quieter scenic places than Mendocino. Both are great.
Id' go with Sea Rock Inn.....of the two.
You can walk into the village from Sea Rock Inn and from there enjoy the walk around the Headlands State Park (2 miles) and get down to the beautiful Big River Beach. The village is peaceful and interesting. Don't worry about the food, just mention that little tidbit when making your reservation and I bet the innkeepers will go out of their way to please you.
Monterey Bay and Mendocino are really nothing alike except they are both on the water. Where are you flying into? Mendo is a good 4 hour drive from San Francisco. Monterey is much closer. How much time do you have to devote? The drive to Mendo is much prettier plus you can stop at the Anderson Valley wineries along the way.
Mendo is a small artistic village on cliffs. Monterey has much more entrance fee type tourist stuff. Do you like to hike and water gaze (Mendo) or visit attractions like the aquarium (Moneterey).
Both are of interest in their own ways.
I can't help on the housing issue, we were blessed with parents who built a house near Little River.
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