1. Muppet Christmas Carol
2. Muppet Treasure Island
They aren't just 2 of the best Muppets films, they're 2 of the best Musicals, 2 of the best comedies, 2 of the best kids films and 2 of the best best adaptations of the source novels ever. Perfect in every way, I don't really care where the other films come in a list, as long as those two are at the top.
The key to making great madcap comedy, much like the Marx Brothers before them. The Muppets are at their best when they have something respectable to totally disrespect. For the Marx Brothers it was the Opera Il Travatore, for the Muppets it was two literary classics.