I visit San Diego and DL together a lot. My brother lives in SD and we usually combine trips. I prefer to fly into John Wayne especially if renting a car. At the San Diego airport you have to take a mini bus to the rental car companies and it just adds time to the whole thing. So my preference is to fly into JW and get a rental car, drive to San Diego and visit and then go to DL and be close to the airport on the way out. I've had to drive to JW from San Diego in the past and felt like I had to leave really early for the airport in case of traffic problems. There is just a lot more that can go wrong between San Diego and John Wayne than DLR and John Wayne. So this is how I've done it in the past.
Day one fly into JW and rent a car. Stay overnight in SD.
Day two go to San Diego Zoo and stay overnight in SD.
Day three go to
Legoland and check into Anaheim hotel/drop rental car back at airport if you don't want it while at DLR
Day 4,5,6 at DL and DCA
Day 7 head for home
We have done this basic itinerary more than one and had it work very well.
A note on legoland I think adults think the park is cool and probably your 8 and 9 year old will like it. Your two older kids might not think it is too cool but I"m not sure. If you do go to Legoland you can usually get coupons for buy one get one free admission on ebay.
You can also get lots of advise on this board about off site hotels. For me I like to be as close to the gates as I can and I want something clean and comfortable. I've stayed both on site and off site. My next trip we are staying at the Best Western Park Place Inn. It is very close and has generally good reviews. Since your kids are older and you probably will have less reason to need to pop back to the hotel you might consider some of the walkable yet slightly more distant hotels. I prefer to be super close.
Good luck planning