I lived in San Diego, including in La Jolla, for 10 years, so I can give some pretty good recommendations.
In La JollaThis is my favorite in La Jolla -
La Jolla Shores Hotel It is right on the beach.
This one is very nice, not on the beach, but just 5 minutes drive from downtown La Jolla.
Hotel La JollaThis is also not in downtown La Jolla, but just a 7 minute drive or so away. It's where I stayed on my honeymoon. Fantastic views of the ocean, and maybe a 10 minute walk down to a nice, more secluded beach.
Hilton La Jolla Torrey PinesThis one is also technically in La Jolla, but not on the beach. But 10 minutes drive to downtown La Jolla. And it is definitely 5 star luxury, if that is what they are after. Fantastic spa.
La Jolla HyattFinally, this is a very cool boutique hotel right in the heart of downtown La Jolla.
Hotel Parisi