Of course, it's subjective and the answer depends on what you like. I've been to Woodland Park Zoo twice and Houston Zoo three times. Both are large, well done, and have nice collections.
To me, the deciding factor would be when are you visiting? Seattle is wonderful in spring and summer, not so much in fall and winter. Houston is never really wonderful, but the weather is much nicer than Seattle in the winter and is miserable in the summer.
If you are into bird watching and are coming in spring, Houston is about an hour from High Island, an amazing spot for migrants.
Also, if you have time for any side ventures, Houston is four hours from Dallas/Ft. Worth where you can find two excellent zoos and a nice aquarium. Seattle has a lot of other things to offer, but I am not aware of any other nice zoos that are close.