Because of this scene, for years I thought that ferrets were marmots. This is not correct though.
The reason The Dude says "Nice Marmot," is because that's what was written in the script. So why use a ferret in the scene then? According to what I have read on the movie, the Coen brothers wanted a marmot but it proved too big for the scene. So they opted for a smaller ferret but never changed the line.