Another San Diego local. Yes, there are a couple of places to park near Sea World, which is located within Mission Bay Park. You'll see them if you look at the aerial photos on Google Maps. The two closest are at boat launch ramps - these are huge parking lots (but don't park in a boat trailer space, $$$$ parking fine).
Still, I would never consider doing so myself unless I owned a beater car. Car smash and grabs are unfortunately common at the boat launch lots. You should do better at one of the nearby beach / picnic area lots, but only if you will be there during daylight hours only.