Nesta is the better player, probably the top defender in the world. Thuram, though, is still one of the top 10 defenders in the world, and IMO he has lost some form after his great season in 2003. I prefer a 2003 Thuram at RB as opposed to a 2005 CB.
Although, I think Thuram is better than Nesta at controlling the ball at the back. Thuram IMO has world class composure with the ball.