I think it would have been Armstrong (assuming he never retired).
I think he'd have won 2006 pretty easily (using whatever program he used in prior years). I expect he would have started to level off a little through 2006 and 2007, but I think he'd have been closer to 2005 Lance then 2009 Lance.
If Contador was at Disco still in this scenario, there'd be no doubt. Both he and Levi would be controlling things for Lance, not working for themselves.
Even if Contador and Levi were on other teams, I think Lance would have still been top 3 in the ITT's, getting say 3-4 minutes on Rasmussen, 30 seconds or so on Leipheimer and Evans, and maybe 2 minutes on Contador. I think Basso, Valverde and the others would all be at leas a minute back.
While I think Rasmussen and Contador could outclimb him, I think at this point he'd still be at least as good as Levi and Cadel. I'm unsure how he'd compare with Basso, but I can't remember Basso every outdoing him on a climb in the Tour so it's tough for me to put Basso ahead. I think he'd be close enough to Contador and Rasmussen on the climbs that he'd win in the TT's.