gosho said that boss of black organizarion is not agasa. also gosho once stated that if haibara will come to know boss identity will get shocked that clearly states that boss is someone closely related to haibara. bt all her family members are dead. so why ghosho stated that "haibara" will get shocked. i mean to say that if boss is someone closely related to haibara then its clear that it will be closely related to conan also as he is closest to her after her family. bt y will only haibara get shocked why not conan. because it would hav been more convinient to say conan will be shocked rather than saying haibara will get shocked. so it only means that boss is edogawa conan. thats why gosho had to say that haibara will get shocked. also i think gosho said that boss is too clever and careful. we all know that the most careful and clever is conan.
actually if conan is boss of black organization then it would be pretty interesting ending and somewhat sad.