It's hard for me to narrow one down, because almost each of them hold something dear to me for one reason, or another . . . GMC was certainly one movie I probably wore out on VHS as a little kid growing up (MTM to a lesser extent); MTI was one of the first movies I ever saw in theaters, so that was quite an experience to behold; both THE MUPPETS (2011) and MMW are movies I saw in theaters as an adult, and the first time I saw the Muppets on the big screen since MTI, though I wouldn't consider either of them being among the best.
I guess, if I had to narrow it down to one, I'd have to go with GMC, because it has so much going for it: the corny, off-beat, absurd, meta-style humor that you come to expect from the Muppets; a great live-action cast with fun cameos along the way; fun and memorable songs and music scoring by Joe Raposo; really neat and engaging action you don't necessarily expect from the Muppets; and the icing on the cake was it was the first feature-length movie that Jim ever directed . . . I would say it's the quintessential Muppet movie.