That's a really tough call. I really can't decide (copout answer I know) for as much compelling dramas and thrillers Scorsese has given us Spielberg was one of the dudes who pretty much trademarked the magic of cinema. The man is responsible for some of the best in adventure, monster, sci-fi etc.
And when he did dabble in dramatic movies like Schindler's List and Munich I think he did a very good job of it, I'm also impressed at how objective he made Munich. In the hands of many other filmmakers that movie would be so much more black and white.
They're both responsible for some of my favorite movies of all time. I gotta say about Scorsese though in the 00s I'm starting to appreciate Shutter Island a lot more now. The ugly green screen effect and soundtrack really lent itself to the 50s b-movie thrillers he was trying to emulate. I think that went over some people's heads but when I finally got what he was going for I loved it.
Aviator is a movie I really don't care for though, it's kind of a long slog of a biopic to me. I liked Departed and Shutter Island a lot more. But I don't like any of his 00s work as much as Bringing out the Dead. All these movies are great and all but his best work has been with stuff like Taxi Driver, Mean Streets, Goodfellas, King of Comedy etc.