Remove unused boards from Arduino IDE
After some more investigation of the IDE folder, I found a text file called boards.txt in the following path.

 [Arduino Path]/hardware/arduino/boards.txt


EDIT: Be sure to make a copy of the file in case you mess up the following part.

Between two series of '#' characters there will be all the information on a specific microcontroller (e.g uno.name=Arduino Uno). Deleting every line of text between the two '#' series will have the desired effect of removing the board from the Tools menu.