Nicodemus is one shrewd rat and he seems to know it all. (But not to actually be a know-it-all, which nobody likes in a rat anyway.) Nicodemus makes a point of saying that the rats don't have such a thing as titles: "You might call him our chief engineer […] as, indeed, you might call Justin the captain of the guard—if we had any such titles, but we don't" (13.2).
But even so, he is the clear leader of the group. Part of his ability to lead seems to have to do with his excellent ability to make sense of what has happened to the rats. He is a great storyteller (remember his description of learning how to read at NIMH? "By teaching us to read, they had taught us to get away" [18.2]. 'Nuff said.) and his stories serve as a guide to the rats as they try to map out their future. Have you ever heard that old saying "You have to know where you come from if you want to know where you're going?" That could describe Nicodemus's philosophy towards life pretty neatly.