TRACK IR! No question in my mind. I've used stereoscopic 3D available on through my NVIDIA video card, it's the red/cyan glasses. It'll work on AH, but not perfectly, it's very difficult to fight using them. The Track IR on the other hand is a blast and a huge advantage (for me at least) once you get used to them. I never fly without my Track IR but only break out the 3D glasses for novelty sake a few times a year.
Now I don't know exactly what 3D you are talking about though, I know they make more advanced systems than those 3D glasses, any more specifics?