Yes! Conan himself could be the boss of the Black Organization. I don't believe the story that Gin gave him a poison which made him shrink instead of killing him. Everybody must have been aware that this drug makes people shrink. Conan must have wanted to collected information about his Organization's enemies (Like Akai Shuichi), so he took the drug to shrink into a kid and be able to move freely without drawing attention to himself.

This is the most suspicious guy among the people in Detective Conan. I guess he wanted to test the new invention of the black organization on somebody so he used Shinichi as a subject. He must have made Gin and Vodka lure Shinichi after them, in order to force him to take the drug. He made sure that Shinichi would never figure about this by making him move to Ran's place. After a while he made Haibara comes to help him in developing this drug, and to to avoid Conan's suspicion he made her shrink, and made up the story of Miyano Akemi death.

Kogoro is also very suspicious. We all know that he didn't like Shinichi because he his deduction power was better than him. So as the boss of black organization, he ordered Gin and Vodka to kill Shinichi. Even though Kogoro has discovered later on that the poison did not killed Shinichi but made him shrink instead, he decided to leave him as he is, because he liked his new nick name, "Sleeping Kogoro", which he couldn't make without Conan. Of course, Kogoro ordered Gin and Vodka to pretend that they would kill him in episode 425 to avoid being suspected.

This famous Idol has been showing up a lot in the series with minor roles, and has been always acting innocent. But you make no mistake if you think that she is the boss. Although she seems to be good in leaving no evidence that leads to her, I think she made a mistake when she introduced Kir to Mouri Kogoro with the aim of misleading the FBI away from Kir. However, she was lucky enough that Conan didn't pay attention to her.