i am not sure what your budget is, but my family and i had stayed at
http://www.paradisepoint.com/ and it is conveint since it is very close to sea world. i think they may even have a car service to take you to sea world. it is close enough that you could even walk there. also there are several kayak shops close by since it is located in mission bay.
this location has a mini kitchen, but you should check with reservations on what they have available for you in terms of silverware, plates, and microwave. i don't remember exactly what they had. also it was nice that it is a bungle-loo type of setting with several pools for the kids to play in.
as far as shopping or eating there is
http://www.simon.com/mall/default.aspx?ID=765 : fashion valley mall close by. we like going there to eat at king fishhouse. and there are lots of other eateries there too and target. (there is a target closer but it seems like a less desirable location.)
i have also stayed a the double tree in mission valley, but you'll have to drive over to sea world but it is not so far, but it is more suited for corporate use.