Has to be Lovetown for me. I'm not sure the band have ever sounded tighter or heavier and Bono's voice just blows away any subsequent performance IMO. Somebody already mentioned Larry's drumming and I've got to agree, he just gives the thing so much drive and propulsion, it sounds properly awesome, a real primal roar. Since then, it's been a bit more lightweight, at least to my ears.
Purely from a performance POV, The Joshua Tree and the Lovetown tours are poles apart. They just sounded so much more acomplished and audacious in 89/90.
I love the ZOO TV and Popmart versions too, the techno twist really brought the song bang up to date and breathed new life into it IMO, but over the last 10 years, I don't think there's been much variation. This is a charge you could level at the bands live performances in general though.
Larry hit on a good point in the From The Sky Down doc, on stage they could be incredibly inconsistent throughout the 80's (and to some extent the 90's too), the pendulum swing was enormous, some nights they were transcendant, some nights-they weren't.
Having learnt their craft, the band are able to reproduce the studio material almost seamlessly on tour. They are now far more consistent, the pendulum swing isn't as dramatic. On the one hand, this is a good thing, but on the other performances can quickly become very repetitive and almost clinical.
I used to love the studio-to-stage transitions, the development of tunes like Bad, Streets, Please, All I Want Is You and even Mysterious Ways was just so exciting, you never knew what you were going to get from night to night. Nowadays I kind of feel that if you've heard one version of Vertigo, you've kind of heard them all.