Our favorite for beach eating was to go to the Subway and get sandwiches that is on West Mission Bay Drive. There is a huge public parking lot across the street and then a short stroll down to the beach to eat. That is the BEST for cheap eats, and it's very family friendly, play in the sand, can stroll along the beach for a long way. It's touristy but we had a blast there.
La Jolla is beautiful, and Scripps Park is beautiful but it's a little harder to get to and the food choices in that area are for sure more expensive.
However, if you want to have ocean time and don't want the sand, go park by Anthonys Fish Grotto, take a harbor cruise around the San Diego bay (they do one and two hour rides) and then eat at Anthonys . It will be more expensive than Subway on the beach but you won't be all sandy when it's done. The USS Midway and Star of India are also right there and fun for more ocean viewing/touring than getting sandy.