Problem with answering this question is that we haven't seen Manu have to carry his team in the NBA as the clear cut no. 1 option all the time. I would heavily lean towards Manu if I had to answer quickly. But, thinking of it deeper, could Manu carry a team for 82 regular season games and deep into the playoffs without the help of Tim and Tony and a great coach like Pop. For all his faults, Stack led the Pistons to a 50 win season (albeit in the still very weak East) in 2001-02 being really the only good offensive option on a team whose starting line-up included Ben Wallace, Chucky Atkins, Cliff Robinson, and Michael Curry.
I truly believe Manu is the better individual talent. And, everyone saw how Manu carried his Argentine team to gold. But, I'm not completely convinced that Manu could carry an NBA team by himself. If you put Manu (in his prime) on that 2001-02 Detroit Pistons team, is that Pistons team better? Does it go farther in the playoffs?
It's a tough question to answer. As an individual talent, I'd take Manu easily. As a franchise player who has to carry a team offensively for 82 games and then have even more pressure in the playoffs to score with three non-scorers in the starting line-up, I can't really say Manu would have been much more effective than Stack was.