There is a possibility that Dr. Agasa could be that guy we all look forward to meeting one day ... but it seems common in a way, to have the fatherly figure or the one who appears to be perfectly good and guides the protagonists be the bad guy. Also, is there a reason why he hasn't done anything to her yet if he sends out all of these members to kill her? Is it so that she doesn't feel the need to run away? But if so, why wouldn't he have sent for one of the members to kill her, or at the very least give away information about her?
Another thing about the boss is that we shouldn't assume he gives off that evil aura Haibara can sense. Gosho once said that Haibara will be surprised when she finds out who the boss is (or so it says in a book I read). For starts, one could assume that it means first off she doesn't sense any danger from him/her, and to be specific, it could mean she trusts him/her or that she doesn't feel he/she has the capabilities or seems to have an occupation or lifestyle that wouldn't make it seem as though he/she were the boss of the Organization.
There could also be a chance that perhaps... the boss is in a similar predicament as Vermouth? What I mean by this is that perhaps the boss also doesn't age... the organization is REALLY old, so that could explain it. The APTX 4869 couldn't have been a possibility due to the fact that if the boss took the APTX 4869, Conan and Haibara would pretty much be exposed. My theory is that either the boss does not know the true predicaments of Conan and Ai but is pretty close to finding out so since he/she is always close to them, or he/she is one of the few people that know their secret, but for some weird reason is taking the time to observe them, with a huge risk that one of them could expose the organization to someone... unless this gets more complex and the boss is actually a part of the police force, like a major officer, detective, superintendent, or some sort of higher up that is well loved and could dismiss their claims easily. That still pretty much leaves about everyone for a culprit. I'd like to think it isn't a child or teenager, but knowing how Gosho works, anything could happen. Anything.
Somehow "Nanatsu no Ko" and those alcoholic codenames, along with the true organization name (which we don't know yet) must all tie into this puzzle. If we were to say that Okiya were Akai, Scar Akai was Bourbon, and that all the members in the Organization were only members, not just the boss pretending to be a simple member, that still leaves a lot of people. It appears a lot of people that are involved in the Organization are very wealthy, powerful, intelligent, and influential people such as politicians, business owners, actors, and professional snipers. If we were to say that the boss probably pretended to be none of these, and tried not to stand out, andwas extremely close with either Conan, Ai, or both, that leaves us with family, friends, the police, and the FBI for big suspects. There are some exceptions, such as Jodie, who was revealed to have a rough past with the Organization, but overall these people seem likely to be on the list. Even those who were only supposedly dead but never confirmed, such as Ai's parents, are still suspicious. Considering that pretty much everyone who is close to those two are fairly young (at the maximum 50), if one of these people were to be the boss, they would surely have to have done something to slow or halt their aging process.