Your thesis statement should reflect the central claim you are making in your essay. Although you currently have a theme you are investigating, it doesn't sound as if you actually have something you are claiming about the theme. The main difference between a theme and a claim is that a thematic statement just says that you will be talking about appearance and reality. A claim argues that something is either true or false.
You might be able to argue that a central motivating force underlying the disconnect between appearance and reality in all of these three works is a dystopian political system. This would be very easy to argue in the case of 1984, as the falsehoods Winston reveals are in fact deliberate attempts of a totalitarian regime to control people through disinformation. In the case of Hamlet, Claudius dissimulates for the sake of power and Hamlet dissimulates for the sake of revenge. In Waiting for Godot, there is no such overt political issue or one of self-interest; instead, the differences between appearance and reality appear to reflect a more metaphysical truth, but you could cast the master-slave relationship into an underlying system of oppression informing the disconnect between appearance and reality.