it should be a tie. i agree with waneko and king james. i agree with waneko about the malone is really good because of where stockton gives him the ball, but i agree with king james in that you can't say either of them are better, because they just played great together.
I don't consider it a tie. I give the edge to John Stockton because his role on the Jazz is far more important than Malone's and Stockton was always better in the clutch. You have to admire how Malone worked hard on his game and improved each season from the free throw line and adding more range to his game. However, Stockton was instrumental in leading the Jazz every night. He was an ironman and did a great job of shutting down the other point guards in the league. In the post season it was always Stockton stepping up to make the money pass, the steal, or hitting his baseline jumper. You can argue either way, but if you put Stockton on a different team he would immediately improve them, similar to how we've seen Kidd improve the Nets.
Word. Stockton remained among the elite pgs (assists-wise) while in his 40s. Unlike the other elite pgs he didn't have guys like KMart, and Matrix finished for him. Malone is at a disadvantage though. In the west, the 4-spot is the most competitive position. He has to deal with tougher guys than Stockton.