Dhoni may be a better captain when compared to Kohli, but I don't think that he is among the best. During the last year's IPL, he insisted on including players such as Kedar Jadhav in the squad, which resulted in many losses for the CSK, in matches which they could have otherwise won easily.
If you remember the Chennai team last year there was no one available for selection other than including Kedar Jadhav, the team did not give any replacement players either and Shane Watson was struggling throughout the tournament and the only option was to include an overseas player and there are limits for that as well and either they had to include Murali Vijay which is not another replacement in the T20 format.
Dhoni can only perform according to the team you get to lead and if you are getting a worse team you cannot perform well above his teams capabilities.