It would almost certainly be "wide-set eyes". Though I can't find any reference for the phrase, I find far more examples of it on a simple google search than I do for "far-set".
And it makes a bit more sense. The distance between the two eyes is a width across the face, and really isn't 'far' by any means.
Bear in mind that this expression isn't very widely-used, and that it is distinct from the other expression, 'wide-eyed'.