In San Diego the places I always hit...
The Blue Guitar
5959 Mission Gorge Rd.
San Diego, CA 92120
(619) 283-2700
The Blue Guitar has a very good selection from low to high. They like to claim that they have the largest slection of Hawaiian ukuleles on the west coast, although I'm not certain of that... especially with Island Bazaar almost literally on the coast, but they do have them.
Moze Guitars
8415 La Mesa Blvd.
La Mesa, CA 91941
Phone 619-698-1185
Moze has a pretty good selection of ukuleles; their inventory may be a little hit or miss. They do have ukuleles made by a local luthier, Fred Shields, that only sells through Moze. Also Moze sometimes has some pretty good used stuff at decent prices.
Buffalo Brothers Guitars
4901 El Camino Real, Carlsbad.CA
Carlsbad, CA 92008
Phone: 760-434-4567
Buffalo Brothers is also in Carlsbad inland from Giacoletti Music. They are remodelling so the last time I was there they did not have quite as many ukuleles, but they still have a good selection. They are a store I wouldn't miss.
Have fun!
John