Phantom Menace. During this time he is in constant practice, confident, and most of all is cool, calm and calculating when it comes to battle. He uses strategy and guile.
After this he gives up all of this for blind rage and fury. Sure his saber skills may have been more honed later on than in PM, but there's no constant practice, no confidence, he's mostly angry all the time and doesn't care, he just throws himself at his enemy. Most of all he loses all of his strategic thinking.
Therefore PM is his prime.