Here’s what I think. Kapil Dev led Indian cricket team win 1983 world cup, people called him the best captain. Sourav Ganguly entered and led the team to new heights. People started calling him the best captain.
Came in MS Dhoni! He redefined Indian cricket with his exceptional batting and style. People called him the best ever captain.
Now Virat Kohli is leading the team. His brief stint till now has been very successful. Now everyone is calling him the best.
My point is, as we move forward and new captains come, they always would do something remarkable on the field that will give them the title of best captain of all time.
So comparing the current skipper with the past one is quite unjust. Because if you’re going to focus on their winning percentage, we must also factor that each of the captains lead different teams in different situations and under different conditions. Some may find winning favorable, others may not.
So yeah, any team captain (at least the ones who donned this hat for long) are great in their own way.
However, just for the sake of answering your specific question, here’s how things are:
On paper, Kohli’s record looks better. He is the first Indian captain to register winning percentage of 80 in ODIs. His-led team has registered more number of consecutive wins.
So yeah Kohli looks better on paper. However, his stint as the captain is fairly short at the moment. As we go ahead, we will see how he faces more and consistent challenges. Can his team perform better on big stages? Can he help his team win big tournaments?
We will see! But admittedly, Kohli looks better than Dhoni. Still I would always pick Dhoni in my dream team.
Virat Kohli is someone who excels when put under pressure or given responsibility. His performances improved significantly in test matches after being given captaincy. Same can be expected in ODIs and T20s as well(hope so).
While on the other hand M.S Dhoni is a person who stayed away from the limelight and shaped the careers of many world class cricketers (for eg Virat Kohli, Rohit Sharma, R. Ashwin etc) and sacrificed his own batting career (he batted at no.6 for most of the time).
We can't compare them because comparing them would be like comparing rock music and acoustic music. Virat Kohli still needs to prove his skills as a captain while M.S Dhoni achieved all the things a captain can achieve.