We have 3 major candidates.

Jason Kidd, Steve Nash, and Cp3

Early 2000s. 2002-2003. Kidd was able to lead his team to back to back finals appearance. (Only losing to Shaq/Kobe Lakers and Big 3 Spurs respectively)

Everyone thought Kidd would be inarguably the best PG of the decade.

However, in Mid 2000s. 2005-2006. Nash was traded from Mavs to Suns. And his partnership with coach Dantoni worked wonders. Unlike Kidd. Nash never was able to lead his suns team to a finals appearance. Usually losing to Spurs or Lakers before reaching the big stage. Still Nash won back to back MVPs in that stretch

Then Cp3 came to the party as a late game. 2006, he won Roy. 2007, he was not even an all star. But in 2008, he had a skyrocket leap. Not only he made all star. He became an MVP candidate!!!. And even placed second place behind Kobe Bryant (one of Top 10-12 all time players)

My Verdict

Cp3 kinda came late. And a good amount of his prime years will be in 2010s instead.

So, it is Nash VS Kidd.

Kidd back to back finals appearance was amazing.

But I will give the edge to Nash. Just because on how deep the wild west in his time.

So, I have (for 2000s)

1.Nash

2.Kidd

3.Cp3

Honorable Mention: Deron Williams