It shouldn't be all that close.
Manu beats Tony in all meaningful categories and once silly things such as per game stats and all star appearances go out of favor like batting avg or RBIs in baseball a player like Manu will shoot up on lists such as these and rightfully take his place among the all time greats.
Whether it was more minutes or less minutes the facts remain that Manu contributed more to his team winning than Parker (and many many others who played more minutes).
He clearly has better career defensive rating, offensive rating, RAPM, defensive plus minus, offensive plus minus, VORP, Win Shares per 48, True shooting percentage and of course also wins the PER though that's less important here.
In the playoffs the picture is even clearer and across the board his impact dwarfs Tony's contributions including regular Win Shares (not just per 48 like regular season) overwhelmingly with 19.3 vs Tony's 12.7
Both are among the greatest Spurs ever but it's a little bit frustrating that much of the mainstream whether the reason is not looking closer at eye-test-level where I'll claim that if you really pay attention you can see this picture or at the best stats available, still sell Manu and his greatness way way short.