Call me crazy, but I think this one is a no brainer. I will go with Hooker on this one.
Hooker, even though he had many downfalls, Hooker was a skillful commander. No one but Hooker can tell what happened when he learned that Jackson was at the exit of the Wilderness. Hooker out generaled Lee with the pincer movement into the Wilderness but failed to capitalize on his gain. Grant basically bullied Lee into submission.
Hood was a wonderful subordinate but he did not have the skill to lead an independent command. This is completely evident when he took over as the Commander of the Army of Tennessee.
OE, you might have said it best, but you didn't.
Both were great Commanders, though they were those who performed best under someone elses guidance.
You mention Chancellorsville, which, if not for a rebel shell shattering a door frame above Hooker's head, would have been his best battle, but it became his worst. Hooker was brilliant in command of the 1st Corps, and served VERY notably in the western campaign. He was a great leader of men, and, with with the exception of Meade, Hancock, Reynolds, and Sedgewick, commanded a corps of the AoP as well as anyone could have hoped.
But thinking that his feint against the Fredricksburg works would force Lee into inactivity was foolhardy. He should have learned that Lee was one to slip the cuffs. Had he temporarily ceded command, there is a good chance that the war ended here.
Hood was a totally different animal. He was Lee's Airedale Terrier, strong and manically loyal. His record as a Division Commander is generally unrivaled, his "out front" style and willingness to face fire led the boys from the 1st Corps, ANVa, to glory that possibly no division before or since has earned. But, following the wounds at Gettysburg and Chickamauga, Davis made a fatal error, (ANOTHER BOXING ANALOGY), Going with the Knockout Artist Hood, in place of the outsized, but faster skilled counterpuncher, Joe Johnston.
The tragic path from Peachtree Creek to Nashville, i blame on 2 things. 1, Hood's natural aggressiveness, both from his psyche, and that there were very few times that Longstreet's Wing/Corps sat on their hands.
The other reason is the Laudanum or Morphine that Hood was surely addicted to after his wounds. I blame this on his 'punishing' of Stewart's and Cheatam' corps at Franklin as a result of their not completing the attack at Spring Hill. Nashville is also a combination of both.
Overall, "Fighting" Joe, would command a Division or Corps in my army before Hood, though every great army needs a Hood.