There are a couple state parks in North San Diego on the beach that would accommodate that size rig but I doubt you'd be able to get in at this late date (San Elijo, South Carlsbad via reserve america). There are three other water front parks that I know of that are closer to down town: Mission Bay RV Park, Chula Vista RV Park and Campland on the Bay.
I've only stayed at the two state parks as they are on the ocean not a bay. I've toured Campland and see no reason to spend any money there. I had reservations at Mission bay but had to cancel for some reason. Of these three Chula Vista seems to have the best reputation. Mission bay is more of an unknown. Campland, well some like it others don't.
On short notice you should stay at Chula Vista RV Resort. It is adjacent to a Marina and a waterfront park. It is deep in San Diego Bay so no waves no pristine views and no beach. All the State Parks will be too small for your 40' footer. Camperland on the Bay is a parking lot on the Bay. Lots of kids. On the Silver Strand there is a State Park that is right on the ocean. It is first come first serve. It has limited space and no hook ups. If you get there mid week there is a good chance you will get a space. They lock the gates after dark. You could go over the Coronado Bridge and head down the Strand toward Imperial Beach and stop at the CG. If full you could continue on and hook up with I-5 and go to Chula Vista RV. Need more info PM me.
The KOA in Chula Vista or Campland by the Bay in San Diego. Campland is right on the water across from Sea World. The sites are kind of close but, for kid activity the place is ideal not to mention the view with some of these sites.
The KOA on the other hand is very clean and has grass in between the sites. There is also more space between the sites as well.
Chula Vista KOA is a nice park. I think the best is Chula Vista Marina & RV Park. They are not far from each other. One's on the water the other isn't.
My family really enjoyed staying at Santee Lakes. Very very clean, family orientated, well patrolled, huge park, fishing, cycling, allow campfires, central location. Check it out:
We just got back from our 1st visit to Chula Vista RV Resort and we were very happy with the accommodations. Very clean and everyone was very pleasant. We will go back again to this park.
'03 Chevy 2500 HD Crew Cab Duramax S/B, Reese 16K slider, Prodigy, Firestone Ride-Rite air bags, HitchHiker II LS 26.5RL, Trail Air pinbox, TrailAir Equa-Flex Suspension