OK, without a better description as what is important to you in regards to in a Hotel/Motel, such as walking distance versus a shuttle, very basic place like a Motel 6 or something nicer. Is a Free Breakfast important. How much do you want to spend.
Since you are planning to have a car, more things to do. I like the Balboa Pier area of Newport Beach for a beach day, and if you think your kids could handle it, a whale watching tour, they are offered year round, and you can find deals for $15 tickets by doing a google search.
http://www.visitnewportbeach.com/vacations/balboa-peninsula/#ppZQhjUVo7UXR2gY.97
I also like Long Beach for the Aquarium of the Pacific, maybe combine the day, start at the Aquarium (The Lorekeets are more hungry in the early hours)ad drive down the Pacific Coast Highway to the Balboa Peninsula.
www.visitlongbeach.com
Carlsbad is great, with
LEGOLAND and other options. (North San Diego County).
www.visitcarlsbad.com
And of course, San Diego.
www.sandiego.org
The Santa Ana Zoo, the Discovery Cube Discovery Center and the Bowers Kidseum are also a short drive.
www.visittheoc.com
So let us know more about what what you are looking for a Hotel/Motel, so we can help with that.