Haven't been to any of the places, but here are my thoughts from info on the Websites:
Jiai Aikido: A bit expensive IMO, and slightly dubious claim of being "associated" with Ueshiba's Aikido. What does that mean? Are they part of the Aikikai or aren't they? If you visit them, find out exactly what their background is.
Aikido of SD: Seems decent. Not as expensive as the first place, are clearly associated with the Aikikai (according to website at least!) and the head instructor credentials seem impressive.
Sunset Cliffs: Again, seems as though the head instructor has v. good credentials. Not too sure if this is Iwana Aikido or Aikikai Aikido though, you may need to check. More expensive than Aikido of SD, less expensive than Jiai.
San Diego Aikikai: Has a great lineage it seems. As expensive as Jiai, but again, seems to have a lot more in the way of credentials.
This is all just from the websites. I would recommend that you check them all out, see what you think. I think they all seem like decent places with the exception of Jiai, which seems the most dubious.
"Let your food be your medicine, and your medicine be your food"