For some reason I only enjoy half of his movies before Gangs of New York. From that movie onward, it's all top 5 of the year material with Hugo and the Departed being my favourite movie of the year they came out. Of his older movies, some are movies I find pretty average for whatever reason. Raging Bull is probably considered the best of his movies that I just can't enjoy. I've given that movie 6/10 in IMDB but even that rating has one or two points extra just because it's a classic and I "have" to like it.
As for this topic in question, it's hard to decide between Casino, Goodfellas, Hugo, The Departed and Shutter Island. I consider Goodfellas the best movie out of those five, but my favourite right now is probably Shutter Island. Or Hugo.