I would go with your gut. A few years ago when we were ther Thanksgiving week, the Friday after Thanksgiving we did Epcot in the morning and then went to Animal Kingdom. Since the parks are larger, the crowds didn't seem too bad.
So choose the park you want to be at, you can;t avoid the crowds. I would choose MK over AK. There are more things to do / more things to swallow the crowd.
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