It's probably the case that as antigravity systems became more and more popular cities were able to be built higher to escape centuries of pollution, maybe lots of other cities have the same issues considering it seems that the flying cars still seem to emit some form of exhaust fumes too so the issue may still continue.
As the water level in the movie seems to have inexplicably dropped it seems that the land around Manhattan and the bridges have been built on, so perhaps it is only a problem with central Manhattan or NY in general, in the wide-angle of the city as the plane leaves for Fhloston you can see the fog surrounding the city where the river used to be, so it might be a case of some of the newer areas were designed to sit 'under' the fog.
One theory was that the entire city was lifted to escape the fog but Luc Besson stated that the ocean levels have dropped because they took it for terraforming other worlds, however this would make little sense as there is plenty of water ice and asteroids to mine in the galaxy
However, it'd be interesting to see other cities in this universe, such as London without the Themes or Venice with multitudes of flying gondolas, although there's no real sustained theory as to why the water level has dropped apart from taking it for terraforming, but I doubt it has any relation to the fog.