Its impossible to judge them against each other, since they played in different poker eras.
Stu was a great reader and player, and won 3 main events - something that will NEVER happen again. However, he was a compulsive gambler, something that may have hurt him when he tried to adjust play due to Moneymaker Effect (all the super aggressive play styles). Hard to say since he has left us.
Daniel is a fantastic player, great reads and great tournament skills, also he has a knack of killer players with kindness, something that is actually hard to do and make it look genuine. I have dealt to him several times and have seen just what kind of sick reads he can make first hand.
I put both in the top 10 for all time tourney players, which is about the best you can rank players these days (except Helmuth who gets a top 5 ranking)
Ending conclusion - you cant place one above the other, two different players, two different times. If Stu was still here it would be a different debate maybe...maybe Stu gets a top 5 draw, and maybe Helmuth doesnt win so many titles.