We use Newport Dunes several times a year.
We look at the higher cost as a deterant to keep trouble out.
Security is fine, (remove ipods ect at nite though) launching is fine and convienent if you're camping there IOHO's.
Not familiar with the trailer rental places, but if it's a better deal than El Monte, we think you're right in considering them. Newport Dunes may have RV rental places they already work with and approve BTW.
Newport Dunes has all kinds of family activities so perhaps check on what's up and maybe plan to be a part of them if they appeal to your kids.
For example:
They have a bicycle parade and the kids decorate their bikes with materials supplied by, and a decorating party held by NP Dunes.
Seems kinda trivial, but it's a BFD to many kids.
Bike riding from NPD to Balboa Island via the ferry is a huge thing to our kids BTW.
We found the Good Sam Discounts wern't worth our mailbox constantly being stuffed with Good Sam Insurance sales brochures and other nonsense Good Sam offers so we lump it and pay the extra 3 bucks.
You can check online or ask NPD what discounts they currently have.
Most their RV spots are simple back-ins, but they do have a few on the beach that are nice but very pricy.
Make the reservation early, they fill up fast. I'd recon probably 50% of their spots already taken by regulars with standing reservations. You can always cancil.
Hope this gives you some idea.
If givin a choice, our kids prefer on-the-water San Diego camping.