If you’re going kayaking in La Jolla cove, there’s an outfit called Hike Bike Kayak in La Jolla (in the Shores area) that does a great job w/their tours of the cove and the caves.
You’ve got some wonderful ideas already, most of which I would second. I’ve got two girls – ages 9 and 14 – but I also have a 12-yr old nephew, and when he comes, his favorite thing is to just go to the beach and boogie board, but it’s because he’s from the Chicago area, so anything beach or surf related is hugely fun and different for him. If your nephew is into surfing (or wants to try) it would be a good idea to give him a surf lesson for 1/2 day to check it out.
I would agree that it’s VERY important to warn him about the stingrays, which are already coming out at Del Mar beach. Shuffle, shuffle, shuffle! It’s hard to warn kids without absolutely freaking them out, but it’s so important because if they’re stung, it can be unbelievably painful and probably traumatic.
If your nephew’s here for a long time (like a week or two) you might even want to enroll him in a surf camp, where he’d get a few hours of surfing every weekday morning or afternoon and be w/kids his own age, and then you could go do other stuff the rest of the day. The surf camp we like is Sol Surf camp in Del Mar, run by a former teacher of our girls. He’s very mellow, a fun guy and great w/kids. I think it’s $250/week. I haven’t really checked out others, but I know there are many good ones and it depends on what’s convenient for you.
Two more suggestions – hang out at the Gliderport in Torrey Pines for an hour or two watching takeoffs and landings (it’s especially busy and fun on a weekend). If you make it a lunch stop, you can also grab a sandwich at the snack shed – we love their BLTs! Also, you might combine it with a short, easy hike in Torrey Pines State Park, like the Guy Fleming trail. I think the trail is only about a mile long, and is flat, and it’s got a great payoff – the amazing view of the ocean, cliffs and coastline, which you’ll come to about halfway around the trail.
Even my soon-to-be 50-yr old hubby loves Miramar Speed Circuit, and kids flip over it, especially around your nephew’s age. There’s another place like that in Carlsbad, which I hear is even bigger and nicer, but I don’t know the name.
Oh – just remembered one more thing that’s a big hit with kids – going to Belmont Park. Yes, it’s very seedy, but if you don’t make it to Disney or SeaWorld, Belmont Park has some fun rides (we love the old-fashioned wooden roller coaster, which really whips you around). The kids also love the game room, of course. Sometimes it’s the lower tech (and less expensive) things that provide them w/the greatest thrills and lasting memories. Belmont Park is also good if you only have an evening or afternoon and can’t make it to the other big attractions, or if you want to combine it with a bike ride along the PB boardwalk to do some people-watching. Bikes rent on the boardwalk for, I think, about $10/hr. so you don’t have to bring your own. Also, you can have something at the Wave House, sit on their patio and watch everyone trying to surf on the artificial wave…that’s always fun and provides a 12-yr old with lots of laughs from watching all the wipeouts. Have a great time!