Neither. It's usually set by X configuration files - try firing up emacs and opening your home directory to see all the "dot-files" (they begin with a . !) Or browse with a file manager set to show "hidden" files. Look for something like ".Xresources", or ".xinitrc" or any file beginning with X.
X *is* the desktop system, and window managers such as Ion run on top of it, as client and server. Wow, not many new users pick Ion! I'm presuming you know a thing or two more than average just based on your choice.
To help you choose a new font (the strings will probably look like a bunch of dashes and asterisks) there's a program called "xfontsel" that should be somewhere on your system. It's a little GUI where you pick font atributes, then you can copy the string it generates into your config files.