IMO Khaled Mahmud Sujon was the best captain.Though as a player,at the time of captain wasn't so good. But his captaincy was impressive. But in his erra the team wasn't so strong. For this he didn't get any significant success.
There was another who is Khaled Masud Pilot during his captaincy erra he was the best performer in the team. In Sri Lanka he was man of the series in an ODI series which was the first in Bangladesh cricket history.
Akram Khan was also referable. We won our ICC trophy in 1997 under him.