Since you are going to have a car, you really aren't going to be limited to a beach in San Diego since all of the beaches from LA to San Diego are at most a 2 hour drive absent horrendous traffic.
Each beach has its own personality -- My favorite is Laguna Beach because it combines the beach with an artistic community as it was originally settled by a lot of bohemians so it retains that character. The center contains nice shops, galleries, interesting restaurants as well as the beach of course.
During August there is an on-going craft fair, art festival as well as the Pageant of the Masters which should definitely be seen if possible -- People posing as famous works of art. I took some kids to the craft thing but they were slightly older -- there were some fun hands on stuff your son is probably too young to appreciate it -- however, I also found when I dealt with young kids that everything was exciting to them -- my niece was just as fascinated by the flowers at a Ralphs shopping center as Disneyland so an outdoor type of thing that is child oriented is fun for both adults and children even if it isn't completely child-centric.
Some days I pray for Silence, Some days I pray for Soul,
Some days I just pray to the God of Sex and Drums and Rock 'N' Roll.