I don't have a set theory as to who it is, but I have dismissed a few characters as possibilities to me.
Agasa Hiroshi: If he had been searching for Sherry, she wouldn't have lasted as long as she has. I don't see how he could have orchestrated the b.o's movements while with Conan or Ai, as in the Meeting With the Black Organization case when Haibara was captured and he was with Conan soon after. He was part of so many cases outside of the Black Org.'s involvement that it doesn't seem plausible that he'd be interested in capturing either Conan or Haibara. Also, he hasn't voiced any suspicions of Okiya, which he would have had he been involved, because if Haibara mentioned sensing a member, he would have noticed that he wasn't a member he knew.
Elena/Atsushi Miyano: As far as I know, they were nothing more than scientists for the organization, and I haven't seen any proof that they are still alive, let alone operating the black organization. Besides, research for the apotoxin drug wouldn't have fallen to Sherry if their deaths had been faked; they would merely have continued their work in secret, although I don't see a reason to pretend to lose their lives.
There are a few others (Kogoro, Eri, etc.) who seem to be completely out of the question. There's almost no way for any of these to be in charge of the organization, especially as Kogoro was nearly sniped by Gin, Eri was living with her daughter and police-officer husband while the black organization was being formed/working.
As for Okino Yoko, while it seems to be a long shot for a pop star to be the leader of a crime group, it's an intriguing theory. It would explain why Vermouth is one of the Boss' favorites, as the two would be close as fellow actresses. It would also give grounds for the fact that she's a fan of Kogoro, as the organization would have been alerted about him during Kir's arc and when they thought he'd placed the listening device. Also, the first case she appears in, in which her old boyfriend commit suicide, would add to the idea, as it mentioned how she had had to leave him when her career took off. (could be that she decided not to let him know any more about her when she got more involved in the group)
Aya Nanakawa seems to me the most suspicious minor character, as she was in the hospital at the same time as Mizunashi Rena, and therefore could have been involved in relaying intel to the organization, besides the fact that her name contains "Nana" of Nana's song/ Nanatsu no Ko. But because she's only a student, I doubt her rank in the organization would be high, as her youth would ensure she wasn't a founding member.
There are a few other people I'm suspicious of, mostly because I don't know the origin of their names, and there are Mobile Suit Gundam characters with similar names.