championships/championship runs: stockton went to the finals twice in his career, GP has been to three but was only top three on his team for one of them. So I give the edge to Stockton.
intangibles: I know a lot of people would say GP for his fire and defense but Stockton was a pain for lots of guys. He would just lay the wood to opposing power forwards all th time despite being a foot shorter.
running their perspective teams: Stockton ran his team as well as one could expect, GP was less effective yet on the defensive side he gave Seattle its identity. So I'd say its even here.
Overall I'd say its Stockton but GP deserves to be amongst the top 10 guards of all time.