Here's is my top 5:
1) Yusaku Kudo - He is obviously smarter and one step ahead of Shinichi even via telephone. And he's the one who discovered the big truth about the BO.
2) Heizo Hattori - The same as Yusaku but with Heiji instead. But he hasn't showed the skills of Yusaku IMO.
3) Conan/Shinichi - Come on, he's just a high school student and does not have the infiltration training, abilities and help of the FBI just like Akai.
4) Shuichi Akai - He is Conan but with +10 years and FBI training.
5) Kaito Kid - This guy is unbelievable. He doesn't has Conan's deduction skill, but he is able to make difficult tricks and robberies that need Conan & Heiji best performance.