While figuring out cost, make sure you price your car rental from each airport.
I don't have experience in doing that, as we use debit cards and therefore don't usually rent cars (they either won't, they run a credit check, or they keep a big hold on the card), but I did once book us into Ontario, thinking the shuttles would all be the same price. Wrong wrong wrong. Over $50 for me and DS to get from ONT to our hotel, while getting from SNA to a hotel was less than half of that.
So check the total price, not just the airfare.
I really liked SNA, it was SO close. The drive from ONT seemed like the longest hottest drive in the universe, and the freeway we took was scary to me.