Well, I have a couple ideas as to how to narrow down who might be the boss. First off, I bought this book, The Case Closed Casebook, which doesn't share a lot of information, but the information it shares on the boss of the Black Organization was interesting. First off, it mentions the boss hasalready been introduced. (Jodie, since this book is commonly discussed in Detective Conan Fan Forums, this is probably what you were referring to, as it states Gosho said this in an interview, though there are no sources in the book telling you where or when)
I did some research to find that the book was released June 29, 2008, so because of this, one can assume the boss was featured before file 640 roughly (It doesn't narrow it down too much, but at least we can exclude recently appearing minor characters). Unfortunately, it is not stated whether the boss is a major character, minor character, or his/her name has been only mentioned before, but the next clue Gosho gives is that Haibara would be surprised if she knew the boss' identity, so one can assume she either knows the person or, if she met him/her one day, she would not think he/she would be suitable enough (too old, young, weak, simple minded,etc...) Finally, the boss' name will be tied to the true name of the syndicate (meaning the Black Organization is not the Organization's true name, Conan just calls them that because that is what Akemi Miyano, a low ranking member in the Organization who knows little about them, told him.
Gin has hinted the boss might be a male. A couple of times, he has referred to the boss as a he, but at the same time, this all depends on how close Gin knows the boss. If he has only talked to the boss on the phone, then the boss may have disguised his/her voice, so the gender would be impossible to tell just from a call, but if Gin was to have met the boss... then chances are the boss is male.
The boss seems to have some connection with "Nanatsu No Ko", the e-mail address to contact them. Alcohol might have some sort of a relation to the boss also.
Vermouth is the boss' favorite subordinate. Why? Vermouth seems to be one of the only members of the Organization that shows true emotion (besides for Akai and Kir, but they're infiltrating the Organization for the sake of the FBI/CIA). The boss probably finds Vermouth to be his/her favorite because of how Vermouth hasn't aged. She looks exactly the same as she did when Jodie was a child, and has faked her death as Sharon Vineyard, continuing life as Chris Vineyard and Vermouth. How old is Vermouth really? She may even be older than what we think, with Vermouth. The reason for her immortality and the large science department probably has something to do with immortality or such. I'm not sure about raising the dead, as according to this handy book I have with me here, Haibara has denied that (although I don't remember that in the series. Then again, it's been a while since I've read the first 200 chapters, so I'm not entirely sure). The blackmail could be for money, the science department could be for the research and creation of something that can grant immortality along with the creation of poisons, the computer software can be for the sharing of data and information regarding what they seek, and the murders are to keep those who plan to reveal their research and expose the organization silent, but that is an unjustified theory, only a mere thought I had considered.
Sorry, back to the topic of who the boss might be (getting off topic here!) If the movies have some influence on the manga (which it has been hinted that the movies do), then perhaps the boss is not amongst the police (think movie 13), but we cannot be entirely sure the manga has some movie influences for sure.
I have considered Dr. Agasa and Yusaku Kudo, two guesses that are commonly made, but I doubt it could be either of them due to their actions. With Dr. Agasa, why doesn't he do anything to Ai or Conan if he knows their secret? Some people believe he is waiting for the right moment, but he has already told multiple members of the Organization to find and kill Sherry, so it makes no sense. As for Yusaku... I'm quite sure at the very least he wouldn't allow his subordinates to drug his own son, or harm him in any way.
Also, the boss is either fairly old (At least 40) or the boss has changed over the years. The Organization has been around for over 20 years, but according to this lovely book here (again), Haibara makes a comment in her thoughts, wondering how "Kudo" would react if he knew he was part of an experiment that was over half a century old (50 YEARS!) Again, I don't remember reading this, but I'll go along with it unless I can prove this book wrong.
Hope that helps!