Our top recommended place to stay in La Jolla is:
La Valencia Hotel: I love this old hotel from 1926, with views of the water, that is located right in downtown La Jolla. The Lobby is a great place to meet friends for a drink or cup of tea and the restaurant is very good. It reminds me a little of the Four Seasons Biltmore in Santa Barbara, but on a much smaller scale.
Also getting good reviews is the Estancia La Jolla Hotel & Spa at 9700 N. Torrey Pines Road and the La Jolla Shores Hotel on the beach.