Absolutely not .The reason for this is ......Ai haibara always has a feeling of fear when she is near a member of BO. Also ,if he was The boss of BO ,why would Gin and Vodka will carry on a very desperate search for ai .Gin is a high ranking member and he would have been surely informed of it .Take the case when ai and gin met on the roof of the hotel .Gin shot Ai and tried to kill her..Why would he do so,if Dr.Agasa the presumed boss of BO hasn't done so yet.So that rules out that Dr.Agasa is a the boss.P.S Shinichi knows Agasa from childhood,and i don't think a criminal mastermind will have much fantasy about children ,which Dr.Agasa has.
And Dr.Agasa would have no reason to not kill Ai and Conan who poses a threat to him.Why would he make new ,cooler gadgets for Conan ,helping him to solve more cases ,thus accelerating his search for BO.There is no possible way that Agasa can be the boss 8-)