You said "distance runner".
I made a similar post a few years back for Bekele vs. Geb. Here, IMHO, are the criteria (although weighting them is a different story):
* Longevity - They beat your father and they'll beat you
* Range - You are great at one event? That's cute.
* Dominance - They win. Always. Shoot for second and save yourself the humiliation
* Records - Self explanatory
* Olympic/WC medals - Obviously the Olympics are the big deal.
So how do we compare the two?
Longevity - Tough call. Both are old and still great. Kipchoge has been top of the marathon pack for longer than Bekele was top of cross-country/track, but it's close. I really don't know how to rate this. Tie?
Range - Please. Bekele. Shut up. No, YOU SHUT UP. It's Bekele.
Dominance - Kipchoge owns the marathon, but Bekele certainly had periods where he was unbeatable. Perhaps a tie? Nah, I'll give it to Kipchoge.
Records - Bekele has set more records and you can't argue with the quality.
Medals - If we just count Olympics and WC, Bekele takes it in a walk. If you want to include World Marathon Majors then I'm going to count Cross Country and he also takes it. Bekele. Done.
Resolved: Bekele is the greatest distance runner.