What model MacBook Pro are you using, and what model display card (GPU) does it have?
Ray traced rendering of extruded objects in After Effects is extremely slow, depending on which GPU you are using. Some of them, including some used by Apple machines, are not directly supported by After Effects. Many people turn to third party plugins like Zaxwerks 3D Invigorator or VideoCopilot Element 3D to work with extruded objects, because they render much much faster.
Adobe Media Encoder produces exactly the same type of output files as the AE Render Queue, it just does a better job of encoding them. It also has presets for creating YouTube content etc.