As far as holidays go Thanksgiving is the least crowded. Not to say it isn't crowded but it's much better compared to say Christmas or Easter, which I actually found to be the worst since it seems to fall around Spring Break time as well. Thanksgiving is a great time to go if you can only go during a holiday/school break time.
As other people have said, use your fastpasses and do things in between to kill time such as the Hall of Presidents, visiting World Showcase, doing the walking trails at AK or just going from shop to shop at Hollywood Studios. There will always be attractions with no wait times even if they're random ones that you wouldn't normally do like Innoventions or Tommorowland Transit Authority. It's a good time to just see the sights. I'm not a fan of waking up early and neither is my family so we've always gone in late morning and stayed until close as opposed to waking up early and getting to the park as they open. The benefits are pretty much the same it just depends if you'd rather stay up late in the parks or get up early.