One way to work around the arbitrariness of city limits would be to only count the population living within a fixed distance of the city center. I would suggest 5 or 6 km, which is approximately the distance that your can comfortably walk in 1 hour, and also (perhaps not coincidentally) the approximate radius of Paris. This would get you a list of dense cities, which is probably what people are imagining when they thing of "large" cities.

Another way would be to count everyone as part of the population of whatever city they are physically closest to, without regard to political boundaries. But this would probably just get you a list of sprawling metropolitan areas.