If your son loves thrill rides - big roller coasters with huge drops, upside down loops, etc - then go to Knott's. Otherwise, you'll have more fun at CA Adventure. Knott's doesn't have a ton of fun rides that aren't big roller coasters and it's pretty much the only reason to go there. CA Adventure has a wider range of rides and things to do.
If you know you're doing Disney, you can probably get a better deal on a 2 or 3-day park hopper ticket than you would on a single day one park + separate Knott's tickets. Fast Passes don't cost money, but you can only have one at a time so choose wisely when deciding which rides you want to get them for.
There isn't really a whole lot to do in Marina del Rey itself, unless maybe you did some kind of boating trip. You'd probably have more fun driving 15 minutes up the coast and walking around Venice Beach, or a bit farther than that and hitting up Santa Monica and the 3rd Street Promenade.
If your son is into it, you might want to consider heading towards downtown LA and going to the CA Science Center. It's a free museum and they have one of the space shuttles there now, which is really cool to see. There are lots of other neat exhibits there too. Right next door is the Natural History Museum (not free, but fairly inexpensive) and you could easily do both in one day.