Let's look at your points:
"1. Winning margins were if I remember correctly way greater than Bekele's."
(not "way greater". You proved yourself that Ngugi had a couple big margins, but avg margin of victory was only slightly larger than Bekele's_ )
"2. No dilution of competition with short course."
(not a valid argument because:
a) bekele beat all those good athletes who supposedly diluted the long course race by moving to the short course, in, you guessed it, the short course race.
b) Bekele winning the long course race the day after wining the short course makes his long course wins that much more impressive. And winning all the short course races makes his x-c versatility and near-invincibility that much more impressive)
c) please point to one athlete who ran world cross short course instead of long course that had even an iota of a chance to beat Bekele in the long course. You can't. Just because less athletes line up on the starting line of a race doesn't mean that the group of those with a chance of winning has been diluted. Goucher running the short course didn't "dilute" Bekele's real competition for gold in long course. RIght? Of course.
"3. World track champs were only in infancy and once every 4 years so more people peaked for World Cross as it was often only global title available in a year." They are two entirely different parts of the year, and anyone with a legit shot at winning world cross would run it.
"4. World Indoors again not that big of a deal at that stage for distance or even middle distance guys."
This is a somewhat valid point at first glance, but can you point to an athlete who did world track indoors instead of world cross that might have beaten Bekele in world cross?? No way. Again, see point 2c above.
"5. Wider range of terrain and more "true" cross country courses."
Not sure about that. Franklin park was hardly a tough course. And Bekele has run some challenging courses.
"6. Less money in the marathons so again typically more of best distance runners would have a crack at cross country."
Less money in marathons & road races = less great East Africans competing in all distance events over all terrains . since the advent of more money in running, more quality east africans are competing now which means Bekele has been battling more top runners than Ngugi ever did.
"Not taking anything away from Bekele who may go on to win many more titles and make debate irrelevant but at this stage I'm still voting Ngugi...."
Bekele also won a jr gold and silver in the long course the next day AS A JUNIOR. If he skipped the jr race that year, and didn't have to compete in the cauldron of Mombassa last year, he might very well ALREADY HAVE 7 LONG COURSE VICTORIES and be going for # 8 tomorrow.
The debate is already over: Bekele is the greatest x-c runner ever.