Well, Game Maker has a 3d game option.
If you are referring to YoYoGame's Game Maker software, it does not have an "option" but you can develop 3D games, I think it utilizes DirectX.
Game Maker is made to simplify 2D game development, 3D games require advance knowledge of the software.
There are no real 3D game makers out there, only tools that let you mix and match models and world elements to create different versions of the same games (like 'The 3D Game Maker').