People do get carried away with the Brian Cox love don't they, as I recall he was only in Manhunter for a brief time. Both great actors but Hopkins got some serious screen time and produced one of the great screen characters.
I think the very fact that Brian Cox made such an impact with very brief screentime makes it even more impressive. I actually saw SOTL a good time before I saw Manhunter - so with me it isn't a case of the first characterisation being better - its just that even NOT seeing Manhunter - Anthony Hopkins' performance still had me quite giggly. I do like the film (but as I've said - I don't think I'd regard it quite so highly if it wasn't for the performance of Jodie Foster). I DO love Anthony Hopkins but IMO SOTL is definitely not the best work he's done.
I do think (taking the WHOLE cast performances into account) that Manhunter is more satisfying film.