Comment by gonzobonzo

The first list appears to come from one U.N. report where they're using completely different standards for different cities - some are using population estimates for the municipality, others population estimates of just the urban core, and others still using population estimates for the entire region.

As far as I can tell, Tokyo is at the top of the list because because they seem to be using the estimates for the entire region. Other estimates for Tokyo's population - even on Wikipedia - are less than half the number listed there.