Someone we haven't met yet. My personal pet boss theory is that the boss will be discovered through a case from Kogoro's past or the like. The reason for this is I noticed that there is a mysterious absence of anything to do with Kogoro's family background. He's a main character and absolutely nothing has been mentioned even in passing about any of his kin beyond Ran.
Comparing the other main characters
Shinichi - Mom and Dad
Ran - Mom (but because she is related to Kogoro no one else)
Agasa - family in general mentioned, aunt, uncle, cousin’s granddaughter
Sonoko - mom, dad, sister, uncles
Haibara - Mom, Dad, Sister
Ayumi - Mom, Dad, (know she is only child)
Mitsuhiko - Dad, sister
Genta - Mom and Dad
Hattori - Mom and dad
The police have less background than other char groups
Megure - ?
Sato - mom and dad
Takagi - ? (I think something might have been said at some point. I'll review.)
Shiratori - know his family is rich, had a butler person (if I remember correctly)
Basically considering Kogoro is in the top three along with Ran and Conan, it's weird his family hasn't been mentioned even once regardless of whether they are alive or not. You would think Gosho would want to write a dramatic case where one of Kogoro's family members is a case suspect or a victim. Considering the length of the manga and that character family related stories are otherwise quite common, I believe this omission is intentional. I can think of three reasons why Gosho would not want to introduce a relative of Kogoro too early:
a.) It would be too big of a hint.
b.) It would call unwanted attention and suspicion where Gosho does not yet want it.
c.) It serves as a major plot key which will enable Conan to solve a very important mystery.
Given that this censorship of Kogoro's kin has been going on since the very beginning of the manga, it would be logical to assume that the reason is pertinent to the overarching mysteries - namely what is the true nature of the Org, who is the boss, and what is its goal.
Also assuming Gosho had some idea what the end of DC should be when he began writing it, he would probably construct the ending so that in case DC turned out to be only sort of popular, he could end it quickly using the available characters which would be Conan, Kogoro, Ran, Agasa, the DB, and Megure. As DC became more complicated in the Haibara and then Vermouth arcs when more characters were introduced, he probably started expounding on the final solution while keeping the original core the same.
There are two main ways I think Kogoro could be connected to the Org:
a.) Someone(s) in Kogoro's family has a critical connection or position in the Org. I do not support the theory that Kogoro himself is part of the Crow Corps, but with the family name "Mouri", and its difficult-to-ignore resemblance to "Moriarty" from the Sherlock canon, I think that this theory concerning relatives on the dark side holds thematic appeal. (Yes, I know about Mouri and Maurice Leblanc, but a double pun is possible. Mouri/(モウリ)/[Mouri] vs. Moriaty/(モリアーティ)/[moriaati] vs. and Maurice/(モーリス)/Moorisu)
b.) Someone(s) in Kogoro's family was a victim of the Org, and that the circumstances/mystery behind it are a major clue to one of the central mysteries like the identity of the boss, or the org's name, etc. Basically this case from Kogoro's past is the case that lets Conan get the info he needs to really crack the Org mystery open.
Summing it up: Kogoro's relatives are suspiciously absent.