Scorsese's best film -- MEAN STREETS. GoodFellas is great, but Mean Streets puts that film into perspective. Mean Streets (celebrating its 30th year of existence) is Scorsese's most personal film, and it deals with his most important preoccupations -- Catholicism, sexual guilt, the Mafia, New York. It is the first time he worked with De Niro. This film represents the first true flowering of Scorsese's artistic genius. Get the DVD, and study every frame and cut of this one.
Taxi Driver is a close second. In fact, Mean Streets is my favorite film of all time, and Taxi Driver is my 2nd favorite of all time.
Going back to Mean Streets -- the ensemble acting by the four main principals (De Niro, Keitel, Richard Romanus, David Proval) is simply the best I've ever seen in any film. These guys seem like they've known each other all their lives, they seem like they all grew up together in the same tight-knit neighborhood.
The camera work, the lighting, the slow-motion, the editing, the use of exisiting music -- Mean Streets is a must-see.