I found your post while searching for info on how to do this. If you put the fonts directory inside your theme then try:
'../theme/name_of_your_theme/fonts/MyFontFile.ttf'
This seems to be at least half working for me. Though I seem to recall I tried something similar to link to a
javascript file and there were some locations in Moodle that were one folder deeper than the rest, and in those areas it couldn't find my javascript.
I got around the javascript thing by using "new moodle_url('/theme/blah/blah/blah')" and for pictures generally you can use [[pix:theme|blah]] and it'll look in the pix folder inside your theme.
However, [[font:theme|MyFontFile.ttf]] doesn't seem to work, for me at least,
regards,
dave
PS (You might get better answers in the Themes discussion, perhaps someone will move your question there?)