Sourav Ganguly took over as the captain after the Azharuddin controversy when the team was in a turmoil, especially in leadership. He built a young team, giving opportunities to Yuvraj Singh, Harbhajan Singh, Virdenar Sehwag.

He was the main reason for India's aggressive approach in cricket

And also it's under his captaincy india started winning test matches outside India. Not series but tests matches.
They were able to compete.

Many argue Dhoni is better. Dhoni who was given an opportunity under ganguly, was completely opposite
He was calm but equally successful
Only captain to win all icc tournaments. He was tactically the best captain and laid the foundation of a very strong team for the future.