James Rye wrote:
James comes from Professor James Moriarty, the archenemy of Holmes. Black stands for the Black Organisation, the favorite colour of the members.
I think this was supposed to be a red herring until 345. Remember, James Black was introduced as a suspicious character along with Akai and Jodie before we found out they were all with the FBI. But the sheer obviousness of the name puts him among my BO Boss suspects, too. Plus, Conan and Haibara talked about his name toward the end of the P & A episode. The only reasons I see for that are either Gosho was trying to connect with the audience who noticed the same thing or the James Black:Prof. James Moriarty analogy will be useful for the finale.
I've never thought of Akemi though. I like it as long as there won't be a sob sister reunion in the end.

Akemi, being the BO boss, would indeed shock Haibara more than having her parent/s as boss/es, who were never around much anyway. There's equal shock from all of them who are supposed to be dead so we're gauging the trust factor here.
Personally, I would be sad if Agasa is the one. But the most amazing thing that could happen is for the boss to be someone nearby Conan, right? It could also be seen as utterly stupid since Conan is a detective who noticed nothing as far as we know. Unless, of course, Aoyama-sensei unleashes his genius to surprise us yet again.