Tough to say, and equally tough to say the '99-05 version of Armstrong would've beaten Indurain in '91-95. So many other factors and variables change over the years - not just doping of course, but training, nutrition, tactics, race routes, etc.
But it's interesting (and fun) to speculate: If Indurain were racing today, would he have become "Miguel Indurain"? If Armstrong had peaked in the early '90s, would he have become "Lance Armstrong"? Impossible to say, but imo probably not, for either - they were both products of their respective times and circumstances, and most likely wouldn't have had the success they did if they'd been racing at other times. Or, to look at it from a different angle, Ullrich probably would've been a 4-5 time Tour winner if he hadn't had the misfortune of his career coinciding with Armstrong's. Which is to say, in so many instances it's as much luck and timing - beneficial or detrimental - as it is ability.
I think there are only a very select few over the history of the sport who would've "dominated" no matter what period they raced (and setting the doping question aside) - Merckx, obviously, but also Lemond, Hinault, a few others (and maybe, possibly Contador, although still a bit too early in his career to say for sure). Totally my opinion of course, but I wouldn't put either Indurain or Armstrong in that category.