I would say Marienburg and Altdorf are very populated but i think there are much more like miragliano, lothern, naggarond and the big dwarven citys. There are a lot big citys.
Just did a quick search and apparently, as far as the sources are concerned, the most populated cities are labelled as 250.000+ cities.
Skavenblight, Lothern and Marienburg are the most prominent ones.
But, considering how Skaven settlements are layered and it's all guessing of how much children of the Horned Rat there truly are, I think it's fairly safe to say that Skavenblight is by far the most populated city.
Skaven spread like rats