I have been to WDW several times during Thanksgiving. In fact my family and I usually go there only during Thanksgiving.
A few years ago, I would say go to MK and try to get a seating at Liberty Tree Tavern for dinner because they had the characters.
However now that the characters are no longer there, my family and I have changed our tune. We love MK, but find it to be a little too crowded on Thanksgiving Day.
We have found that Epcot is great for Thanksgiving Day since it is such a big park, and many people flock to MK. Epcot is not that crowded.
That said, Garden Grill in the Land is a good Place for Thanksgiving dinner. It's pretty close to traditional Thanksgiving Dinner. It also has Pluto, Mickey, Minnie and Chip 'n' Dale.
We have had good experiences at Garden Grill on the whole.
That is just my opinion. I think Epcot is the better park because of size.
Whatever you choose, have a good time!
-Johnny