I don't understand why so many people are having trouble understanding the question. It's not a very interesting or meaningful question, but it seems pretty self-explanatory. Is the word "best" difficult to understand in all areas, or just when applied to musicals?
I'd say Les Miserables if it didn't end with Fantine and Eponine taking Jean Valjean to heaven.
I'd say Rent if the score was a little tighter and it didn't end with the ensemble singing about waking from this nightmare.
I'd say In the Heights if the book didn't have so much lame sitcom-y dialogue.
So, Avenue Q it is. It's pretty much perfect, and maybe the most important musical of the 21st century.