Trailer parking is a problem in San Diego. Here is what we've found.
Shelter Island Boat Ramp. Trailer parking for 3 days. No dock next to launch site, dock after you're in water.
Coronado/Glorietta Bay Launch Ramp. Daylight parking only. Dock where you can launch.
National City/Pepper Park Launch Ramp. Daylight parking only. Dock launch.
Chula Vista Boat Launch: Daylight parking only. Dock launch. If you're staying at the Chula Vista Marina (nice place,) they will store your trailer for a fee. We paid ~$45/day, boat+trailer, truck was free.
Shelter Island Harbor Patrol Dock. Cheapest place to keep your boat, though we haven't been there in years.
Southwest Yacht Club. Best place to stay if your yacht club has reciprocals with them. Ours does.
Mission Bay South Shores Boat Launch. I think it's three days limit on parking. Dock launch.
Mission Bay Dana Landing. I think it's daylight parking only. No dock launch.
Note that we like to launch where we can walk the boat off and on the trailer.
Also San Diego has limited anchoring area. I believe you can anchor next to Southwest Yacht Club on weekends. Also at Glorietta Bay for 72 hrs, if you make a reservation.
Oceanside. You can store your truck/trailer in the parking lot on the other side of the RR, free. Dock launch. No anchoring
My experience, yours may vary.
Boris