As I mentioned in other forum topics, in my opinion, Okiya Subaru is indeed Akai Shiuchi and "Scar Akai" is Bourbon. Today, I'd like to discuss some hints as to who I think is the boss of the Black Organization.
The first three facts I will list are sourced from The Case Closedjavascript:mox(); Casebook: An Essential Guide. The book claims that Gosho Aoyama has said:

The Name of "That Person" has already appeared in the manga in some form. This could imply, and makes it likely that this person is a frequently appearing person, setting off rumors as logical and as silly as can be.
Haibara would be shocked. By this, we can imply :
the boss is close to Ai.
this could mean she does not expect the character to be able to be the boss becauase:
The person seems useless: Can't seem to do anything at all
The person seems weak: This person is not strong or powerful to what the idea of the boss may seem like
The person seems stupid: This person does not seem to have the brains to run an organization (The first people that comes to mind are Kogoro and Yamamura ;))
The job/occupation does not make it seem like he/she is the boss: A police officer, an FBI/CIA agent, etc...
The boss is a relative: Because it's Haibara we're talking about, this fits into the "thought to have been dead" category, since her whole family is dead.
The boss is related to a protagonist: Although unlikely, maybe something as random as Shinichi's mom or Genta's dad could end up being the boss...?
The person seems too young (a child perhaps?): If so, maybe the boss has shrunk his/herself into a child...
The person seems to old (a 90 year old grandpa? ): I have no clue why it would be this, unless you considered Dr. Agasa, but he's only 50 years old anyways, so he's not old... but that doesn't mean I'm excluding Dr. Agasa as a possibility, only from this category, since he's not old...
The person was thought to have been dead: Perhaps the dead are not truly dead after all.... (I'm not just talking about Akai Shiuchi.)
The True Name of the Syndicate is tied to the Identity of the Leader: Knowing Aoyama though, the name is most likely not direct. More than likely it is multiple words poetically used to leave a large hint as to who the boss of the Organization is.
Now, some facts that have been featured in the series already:
The Song "Nanatsu No Ko" is used to contact the Boss of the Organization: The Song "Nanatsu No Ko", which has been translated to seven baby crows, seven children, and seven year old child, is the contact for the Boss:
Lyrics:
karasu, naze naku no
Crow, why do you cry?


karasu wa yama ni
kawaii nanatsu no ko ga iru kara yo
Because it has 7 cute kids in the mountain

kawaii kawaii to
karasu wa naku no
crow cries "kawaii - kawaii"

kawaii kawaii to naku n da yo
"kawaii - kawaii", it cries

yama no furusa e itte mite goran
marui me o shita ii ko da yo
Go to its old home at the mountain,
and you will see its round-eyed, lovely kids

The song, which uses the notes Si la so la Si la so la re mi re do re mi so la for the beginning, have brought Conan to discover the boss' e-mail. This says that the boss is from or has lived in Japan for a long time, since only Japan commonly knows this song.
The boss uses alcoholic codenames for members: Maybe the boss likes alcohol, or maybe the boss relates alcohol to death or darkness, something the Organization is known for. It's also obviously used to cover up their real names.
The Boss makes the Members wear black: The black Organization is known for wearing black like crows, maybe having some connection with the Nanatsu No Ko song. Black is known to be a mysterious color that can hide things, and keep things hidden in the shadows, also known as the color of death to some, which may be a symbol. Black also can make people stand out less, well, that is, if they don't wear too much black.
The Boss seems to have a lot of knowledge on mysteries: Passwords and codes in the organization have a lot to do with mysteries, for example, the password Sherringford, one of the names Sir Arthur Conan Doyle considered before deciding on Sherlock Holmes. Maybe the boss enjoys mysteries and puzzles, or maybe he/she knows a detective or mystery freak...
The boss takes extreme caution: When it comes down to it, the boss tends to be extremely careful in what he/she does. Even Vermouth noted this in file 704
Vermouth is the Boss' favorite: She gets independence in what she does because of this. But why Vermouth? She's the one who helps Conan and Ran, and seems to even want the Organization destroyed possibly, as she seems happy every time Conan does something that hurts the Organization. Is it because she never ages? Probably not. What about the fact she has sympathy for Conan? This is a killing, evil organization who's secrets can not be revealed no matter what it takes, so no. Also, the boss tends to control Gin a lot, even though Gin will be so loyal and ruthless when it comes to killing, never having mercy and always secretly finishing the job.
The Boss fears Akai Shiuchi. He calls Akai the silver bullet. He knows Akai can take down the Organization easily if he wanted to. Although, now that I think about it... Vermouth also believes the Organization has weak points, whereas Gin believes the Organization will never die... could that be a reason?
The Organization Is pretty old. Twenty years ago, Vermouth was working for them. Some translations of episodes 130 and 131 have even shown Haibara saying the Organization is over 50 years old. What does that mean? That means one of two options: The boss is over 68 (seeing that no child would run an evil Organization, so more than likely the boss would start at a minimum of 18 years old), or the Organization has had more than one boss, which seems more likely, although nobody has mentioned this (but we barely know anything about anyone anyways)
Some quick Organization notes:
The Black Organization created the APTX 4869 (Atsushi and Elena Miyano were the first who were told to try to create it, Haibara eventually created it)
They have a strong science field
They are tied with computer programming
Someone likes mysteries and Holmes
Computer virus Night Baron
Some members have very public jobs, such as acting.
They're obsessed with finding traitors
They usually kill people and make it look like suicide or natural death
They love guns
they have alcoholic code names
They wear black
Akai refers to them as wolves.
Akai is their weak point
Vermouth believes Conan is their other weak point
They have connections in America
They commonly blackmail people
They trick people into believing they're someone else then kill them
Vermouth's the favorite
Gin is a little too loyal.
So, who do I believe the boss of the Organization is? I won't leave an opinion (though I have a few theories of my own), but you should try leaving an opinion in the comments. Even if it's just anonymous, that's great!
Tell Us who you think the boss is!