This guy does all generals, not just the Civil War. He takes the baseball concept of wins above replacement (which gives an appropriate acronym):
Ranking Every* General in the History of Warfare
towardsdatascience.com
Anytime I see something like this it reminds me of the famed old saw -
There are Lies, Damned Lies, and Statistics (full disclosure: I spent more time as a Budget and data analyst that I care to admit).
Number mean a lot, the don't mean all. In the case of Generals there is one non statistical factor that outweighs all else. Did he win? Full Stop.
Not "Yes but..." Did he win. Full Stop. Napoleon is probably the best example of this. "Best Ever?" The same officer who destroyed his own army through sheer hubris? Nope.
To get back to the thread question this is also where Lee utterly fails, much worse than Napoleon. Lee had one job. ONE. Survive (some would argue protect Richmond, which is valid, but misses the point). Lee had to do the same thing as two other, vastly superior commanding generals, he had to maintain a credible force in the field. As long as an actual Army of Northern Virginia was in the field the Confederate States of America were an actual tangible thing; the moment it wasn't the Confederacy was a memory. Washington understood this, almost two centuries later, another general, also fighting one of the World's super powers, Võ Nguyên Giáp understood it as well. Both understood, as Lee did not, that their real job was to stay on their feet, to out last the enemy. Just stay there and make the other guy bleed until the mothers and fathers and merchants and bankers compelled the enemy's government to pick up their ball and walk away. Anytime Lee advanced his main force beyond his primary defensive works outside of Petersburg he was failing to do his only job. He could surely send Jackson or Longstreet or A.P. Hill, or the glory-seeking J.E.B Stuart North to raise hell and terrorize the countryside as long as they had to obey on ironclad order (on literal pain of death) "do not be drawn into a set piece battle against a superior enemy force".
Lee's ego failed to allow him to do this. He escaped the first time, at Sharpsburg/Antietam thanks to the stunning incompetence of McClellan who let the war slip through his overly frightened fingers on the bloody September Day, with most of his army intact. He should have learned from that near disaster. He didn't. Less than 10 months later he allowed his forces to be drawn into a meeting engagement against a superior force operating along interior lines of communication without any real knowledge of the disposition of the enemy force. He then, of course, compounded the error by failing to regain control of both the battle and his own emotions and made two full days of head on charges into prepared positions despite being deficient in artillery, manpower, and lacking sufficient knowledge of his enemy dispositions, state of supply, and ability to reinforce. Lee shattered the single most powerful, and handily best equipped and led, force his nation possessed in a pointless, utterly needless, and more or less hopeless offensive when his ONE JOB was to keep that force intact. Again, his error was somewhat hidden by yet another Union commander who was insufficiently aggressive (some would argue overly casualty adverse) who allowed the remnants of his command to escape, despite being trapped against a river, in "Red" level of supply, especially munitions, encumbered by huge numbers of wounded, and with most major formations rendered combat incapable by absolutely incredible losses, not just in enlisted personnel but in regimental, brigade, and even divisional commanders (Lee had FIVE Brigadier Generals KIA, 10 WIA, 3 PoW, all told EIGHTEEN Brigades lost their CO, four of which lost BOTH the CO and his deputy commander). Meade let him get away. Civil war should have ended by August 1, 1863.
So the first thing to look at is winning. The second thing to look at is effectiveness. Here three officers stand out - Grant, for obvious reasons. Sherman, for understanding exactly what sort of war he was fighting. Nathan Bedford Forrest, for perhaps less obvious reasons.
Forrest, despite his manifest personality flaws (including being what, in later years, would be considered a Category A War Criminal) was brilliant, arguably the best cavalry officer of the war, rarely defeated and never defeated by equal numbers of Union troops. He tied up several times his number of Union foces throughout the war, always keeping a credible force in the field. Forrest was a right bastard, certainly deserved to be hanged by the standards of the era (although he does deserve credit for telling his troops that their duty after surrender was to obey the civilian authority, he loses it for establishing the Klan, despite his later repudiation of the monster he had created) but he was one hell of an effective officer.
Lacking both of these ingredients, no matter what sort of stats they put up pulls a general officer off any "Greatest' List.