or he could be saying good job sarcastically 
even if this is for a mockumentary, i don't really know what kind of point it would be trying to prove....."hey guys i came on stage pretending, convincingly, to be all drugged out and you guys believed me! uh.....got you!"
nah, watch it again you see Joaquin take his glassess off and give him a warm hand shake and the tone of Letterman's voice suggests he was being sincere.
I'm sure Joaquin has a point to make in all this, will just have to wait for the documentary to be released. I think it'll be a really cool and funny experiment to see an actor stay in character constantly for a whole year, the documentary will be more like a movie in that respect