To me the only way to compare players from different eras is by contrasting how they did against the competition they faced.
By that criteria, Staubach was clearly the better QB of the two as shown by the numbers Joseephuss posted.
Both guys played in an era when there were several other great QBs:
Staubach: Bradshaw, Tarkenton, Namath, Anderson, & Stabler.
Aikman: Young, Marino, Elway, Kelly, Moon, & Favre.
The difference was that Staubach was the best of the bunch while Aikman was at best 4th and more likely 5th. I can't rank Troy above Marino, Elway, or Favre, and Young & Moon were every bit as good as he was, Kelly was a little bit behind but not much.