In PyCharm 2016.3, the console font setting is squirrelled away under Settings > Editor > Colors & Fonts > Console Font:
Note: Changes to the colors and font are not visible immediately, you have to restart the terminal session to apply them. It’s not enough to just hide and reopen the terminal. Just click the red cross button on the terminal’s toolbar (Close Terminal Session) and reopen it. The same is valid also for the Python Console.