Some of those stats can be very misleading. JT has played 33 Tests so far. Joey played 24. So of course Thurston will have more wins. I believe win % is a greater guide.
I can't find the stats but I'm pretty sure Joey has a better win % at club level, by a comfortable margin. Hence all the top 4 finishes on the ladder fo the Knights compared to a paltry and quite staggering one for JT at the Cowboys.
Win Percentage
Johnathan Thurston 90.6%
Andrew Johns 86.9%
Keep in mind, the drawn game from the 2009 Four Nations counts against JT's record, where as all of the results that count against Johns' record were losses.
And yeah to illustrate the club win percentage.
Johnathan Thurston: 57.3%*
Andrew Johns: 65.6%
Which is why I can't really see an argument, especially since Joey lead his club to two premierships where as JT participated in one.
Having watched that Grand Final again, I believe his performance was underrated some considering it at least got Anasta off the field. He was awful that night and it was one of the least deserving performances I've seen in some time.
Getting back to the Test point, while it is unfortunate on Johns' part, I believe the fact that JT was able to play more games and achieve more wins while maintaining a better win percentage makes him the better player in that arena.
The only argument in Johns' favour is that he won more World Cups than JT, 2-1. Everything else is in JT's favour.