We have just been to both SeaWorld and San Deigo Zoo...
I loved the zoo: pandas, elephants, hippos (my personal favourite), polar bears, so many fantastic animals.
SD Zoo is on a difficult site - we went with grandma, and she was struggling with the hills (it is on a site shaped like an ice cream cone (or a volcano crater)... a rim around the edge, and the centre lower down... So, if you are pushing a stroller, or aren't very fit - then SD Zoo will be a struggle...
Personally, if you had to choose, I would pick SeaWorld - there are exhibits there which I couldn't see elsewhere (not easily)... LOVE LOVED LOVED the killer whales; dolphin show was great, really enjoyed the sea lions...
plus turtles, white whales, polar bears, sharks, etc etc
Except for the pandas, I had seen all the animals at the zoo before... So, I would pick SeaWorld...
Either way, you are going to have a great day; so you have the advantage of having two great choices