How to remove an object (Tooth) in After Effects
Unfortunately, the only answer is rotoscoping.  You have to remove the tooth from each frame manually.  Rotoscoping tools will help give a closer starting point, but that kind of object removal where both the object and the background behind it are changing and moving is nearly impossible to do without manual effort.

Note, if everything in the mouth behind the teeth is black or basically the same color, then you have a lot more options as Brett outlined in his answer.  I was assuming that there was more detail in the mouth based on your description that would require background painting, but if you can avoid background painting for the mouth, then rotoscoping isn't needed.