I see it coming down to Leo vs. Raphael with Leo winning an epic fight.
ITs on youtube, all of it. I highly recommend it. Mikey is the best, its shown repeatedly. He wins the Battle Nexus, but he faced Raph whose anger got the best of him, and splinter who let him win. But later on they are training in a "Danger room" like the Xmen's and it was Leo and Raph vs Mikey and neither could lay a finger on him. Even after that there was is Robot version of the Shredder called Cyber-Shredder, and he was beating Leo, Raph and Don all at once, then Mikey swings in and literally stomps him solo.
Leonardo is the leader of the group. He trains the most, works the hardest and is as a result a very skilled fighter. He is the most serious of the bunch. He hates Raphael's bad attitude.
Leo always seemed like the most skilled turtle.