I'd like to see Mean Streets on the list, but it doesn't mean I'd vote for it.
Scorsese has made dozens of movies that are on my "top" list. The Last Temptation and Kundun are among my favorite of his best "non-mafia" flicks.
Bringing Out the Dead is a great example of great direction/bad acting. Nicholas Cage and Patricia Arquette are horrible actors (HORRIBLE). In the hands of a director such as Martin (we are on a first name basis, btw) he managed to channel their mindless and over the top acting into characters that were at least decent.
My hatred for Nicholas Cage is rivaled only by my hatred for Leonardo DiCaprio... and Cameron Diaz. They are easy on the eyes but they had some real problems with fleshing those characters out in Gangs of New York. Daniel Day Louis is the exact opposite. He freaking nailed butcher bob dead on. He played the over-the-top character to perfection.
As far as his DiNiro films go, I hold Mean Streets in very high regard. It wasn't as much a "mafia" movie as it was a gang of mooks that had a pretty tight grip on their neighborhood and not much else. Keitel's performance was his best until Tarantino came along and gave him The Wolf. DiNiro was brilliant as the uncontrolable man-child. They were more of a family than any of the real mafia families to come. Take the family out of it and you get Taxi Driver. DiNiro made the man-child a bit more of a hardass psychopath and boy... was it great.
I loved Goodfellas. I also loved it's sequel (Casino), but I'll leave that for the mafia fanboys to discuss.