Plans change, and Gosho didn't even expect Detective Conan to last, let alone go on for 21 years - While the boss has "appeared", I don't think we know if it's just a name, or a full on appearance.
In any case, I don't think it would be either of the Yokomizo brothers. Not only is there nothing to really suggest this, but both brothers seem to have a strong sense of justice, and don't really seem to be nearly capable as one would think the boss should be. They don't seem nearly as experienced, or even old enough to be running a crime syndicate (or soulless), and I think can further be disproved since they are twins. Not to mention Sango has several "odd" traits, and is constantly fanboying over Kogoro's deduction ability (but so does Yamamura).
I don't think the boss has had any close interaction with Haibara, or has even seen her since she has shrunk. Both Sango and Jugo have got a clear look at the girl. Had they been the boss, I'm sure they would have been able to piece something together, or at least had enough suspicions to investigate. At least this is the sensible theory since quite a few characters have already been able to identify her simply by looking at her, and the members of the organization should definitely know her image as a child (Pisco and Vermouth both knew).