Obviously, my gut says Patton. I just love that guy.
And, being a Southerner, I'm gonna piss off a bunch of my brethren and say RE Lee was overrated. He still believed in Napoleonic warfare, when technology made it obsolete. Give me Longstreet any day. Heck, if Lee would have listened to Longstreet about Pickett's charge, things would've been different.
However, I am gonna say the BEST general was Duke Wellington. Man, I love that guy.
Anyway, I think that it's important to qualify the attributes of generals. Alexander was a great heroic general, but that type of generalship would be suicidal now. Patton and Napoleon are great examples of generals with charisma, and neither fit into the 21st century ideal of an apolitical general. Who is the best? I think Wellington, but even by saying that, I acknowledge that he is the best compared to his time. Comparing Wellington to Alexander, Caesar, Grant, Stonewall, Ike, or Sun Tzu is like comparing apples to oranges. The nature of leadership changes, so the role of "general" has evolved over time.
IMHO, Napoleon beat Wellington the one time when he was in Spain and would have cleaned his clock if he wasn't busy in Russia. Napoleon's Marshalls in Spain were egotistically uncooperative and vainly refused to cooperate with each other to defeat the British. Napoleon would have stopped that nonsense in a heartbeat.
Yes, Wellington beat Bonapart at Waterloo. But you have to realize that almost all Bonapart's best Marshalls were dead. Almost everything that could go wrong, did go wrong and Napoleon STILL almost beat Wellington, who himself admitted the battle was "a close run thing."
The extent of Wellington's personal command at Waterloo didn't really go beyond reverse slope tactics, and trying to keep his Allies from running away. It wasn't so much Blucher who won the battle for Wellington, as it was Grouchy marching and counter-marching, completely failing his orders to prevent the Prussians from assisting Wellington AND failing to "march to the sound of the guns" and assist Napoleon at Waterloo.
You can bet that if Lannes or Bernadotte had lead those Corps, Napoleon would have defeated Wellington at Waterloo. I am convinced.
Wellington won the day and he earned it. He was more than competent. But I don't understand why any one would consider him a great General.