This question was in my head for the longest! At first Thought was my favorite emcee because he has the best flow of ANYBODY. No one can touch his delivery in my opinion. However, when I started writing myself I started liking Common better. Com touches a lot more topics than Thought does. I believe Com is the best point blank. But each emcee has their own category. I see it like this:
Black Thought: The Emcee
Common: The Thinker/Author
Andre 3000: The Poet
Nas: The Storyteller
etc. So it's kind of hard to pick who's the best. It all depends on who "you're" feeling. But since the question was on who's the better "emcee" I'll have to go with Thought. I do however like Com better. I like Andre 3000 better than both of them, only because he looks for new rhyme forms when he writes his verses (i.e. Gasoline Dreams, So Fresh, So Clean, Red Velvet etc.) plus he vocalizes.
Peace & Love Y'all

"I'm feeling better than ever what's wrong with you?" -Andre 3000