For at least one special dinner, do go to the Stonehill Tavern at the St. Regis Hotel in Laguna Niguel. It's really quite excellent.
For lunch (and I'm apologizing for picking more upscale places), definitely go to the Montage Hotel in Laguna. Go early on a nice day, enjoy the absolutely jaw-dropping view, then grab a table for lunch at the very casual restaurant on the outside deck by the spa.
For breakfast, also in Laguna Beach, try Cafe Zinc or the Cottage. Both are local institutions and very good. For lunch or dinner, Laguna Sapphire is really quite nice (also in LB).
Laguna Niguel and nearby Laguna are not great restaurant towns, so if you don't mind driving about 20-25 minutes, you will have many more choices in Newport Beach.
In Newport, a spectacular and somewhat divey restaurant right on the sand is the Beachcomber. Because of its setting, it's tough to get in. Don't try it on weekends unless you are prepared for a long wait (no reservations!). For a weekday meal (B,L,D) you will not find a similar setting anywhere nearby. Definitely worth the short drive for the amazing setting and very good food and drink.
A spectacular sushi restaurant in Newport Beach is Bluefin by Abe. It is in a league with Nobu, and is very expensive but worth every cent.
Also in Newport, consider trying the Crowbar and Kitchen. This is a pub-like restaurant with wonderful small dishes.