1. Taxi Driver - Top 5 Film All Time. Personifies everything great about movies from the 70's. DeNiro's Greatest performance. Bernard Herrman's legendary final score. Scorsese even has a great acting moment in it. A guy even claimed that he tried to assisnate the president because of this film. It's as good as cinema gets.
2. Goodfellas - His best work purely in a Directorial sense. So many risks that work perfectly(the famous Copa tracking shot, people talking directly to the camera, freezing frames, ect) and would just be corny in the hands of anyone else.
3. Raging Bull - Pure Self destruction put on film with a totally unflintching eye. No sentimentality to be found.
4. The Departed - This film combined everything that Scorsese's movies are best known for. Gansters. Great combinations of Rock/Pop Songs. Great Performances. Homagaes to classic films(The Third Man, Psycho). Fanstasticaly crisp script. And it contains DiCaprio's best performance to date.
5. No Direction Home: Bob Dylan(Documentary) - Personal favorite here. At 3 1/2 Hours, it only covers the first 6 years of the career or an Artist that totally changed Music as we know it. It is probably the definitive revelatory piece of documentation about Bob Dylan's early career. It's Excellent in every sense of the word.
Honorable Mentions:
"The Last Waltz" - The Greast RockDoc/Concert Film ever made. Bar none.
"The Last Temptation of Christ" - The Controversary that surrounded the film never quite allowed it to be properly appreciated. It's a great question presented in Jesus's character, that most Christians won't even entertain.
"Mean Streets" - A young and raw filmmaker clearly just starting to find his footing, but showing greatness is coming soon.
"Gangs of New York" - Daniel Day Lewis's performance is so good, and so dispicable, that it practically wouldn't allow the Academy to award Lewis as Best Actor, even though he clearly was the best of the year(instead giving it to flash in the pan Adrian Brody)... Still many missteps plague the final film(miscasting of Dicaprio and Diaz), underutilizing of Liam Neeson's character, ect. By all accounts the production of this film was very difficult, and helped add to the result of it being a flawed film. But at the end of the day, the shot of the Towers at the end really brings the weight of the film into perspective.