Stockton completely owns one of the major statistical categories in all major sports. It's one of the most unbreakable records. He's also the all-time leader in another statistical category. Also, the team he quarterbacked won more games than any other team during the 90s.
Anybody who doesn't think he belongs in the conversation is dumb.
The argument against his inclusion invariably comes down to championships. I watched all those games; he certainly wasn't the reason the Jazz didn't win. The number of championships is an important metric, but it is over-used in arguments of this kind. For example, Kobe has 3 of Shaq's rings, and 2 after the Lakers paid for a squad of all-stars. It's hard to hold his 5 up against Tim Duncan's 5 and say "equal". Duncan's mean more. Etc.
Nah, what it comes down to is that at his best he wasn't good enough for this discussion. Stockton was very good for a very long time, but I don't think I'd say he was ever a top 3 player in the league, let alone the best.