I grew up in the north county of San Diego area and have watched (from AZ) the population explode and areas that used to be 'quiet' (North County; Oceanside, Carlsbad) become VERY crowded during the summer. Mission Beach is a nice area, but lodging will be pricey, Carlsbad is extremely nice, again expensive. I would try and find a VRBO (house, condo) in North County, unless you're looking to hit the attractions in San Diego proper. At least with a house/condo, you can cook/bbq and save a little $$ on food. Carlsbad has some amazing beaches, restaurants and it's a little more low-key than San Diego.
Hope this helps!