Jackson, Longstreet, Cleburne, Forrest, Johnston, Hill, Stuart, Gordon? Who is your number one (and two)?
IMO, Lee is the whole package. He inspired and loved his men.
Strategically, Longstreet had the answer to solving Jeff Davis's larger problem, and he proved it with only half his corps at Chickamauga. OK, so they caught the Union line redeploying, but the general idea was the right one. Run the Unionists ragged, and hit 'em where they wasn't. Same thing in scale large that Jackson did in the Shenandoah Valley, plus Longstreet's troops got to ride the train instead of being force-marched until they couldn't fight (which Jackson did when he came down to join the Peninsula Campaign -- he himself was so tired from the march that he fell asleep with food in his mouth, and his troops were no good until the next day).
Second would be Grant. He was, simply, better than any general the south sent against him. He was stubborn and determined, took chances when necessary, knew what it would take to win and didn't let anything deter him from that. If he didn't quite demonstrate the daring that Jackson did, it's because he never had to. But crossing the Mississippi south of Vicksburg, cutting himself off from his supply source, came close. No matter where Grant was, he won. Lee would be third. He was an able general but in many ways an unimaginative one. As I said before, Jackson made him at Chancellorsville, a victory which Lee considered incomplete. It was the very fact that he didn't destroy the Union army at Chancellorsville that made him take the steps he took at Gettysburg, with fatal results. Another fact is that Lee lost to lesser generals, Meade and McClellan.
Longstreet was a capable corps commander, but was he better than, say, Hancock or Sedgwick or many of the other Union corps commanders? I think not. In all his independent commands he failed miserably. If Jackson made Lee, then Lee made Longstreet. Johnston, I assume you mean Joseph, spent the war getting kicked around by the Union generals sent against him. Hill, I assume you mean Ambrose, was a barely adequate corps commander, the other Hill, Danial Harvey, wasn't a lot better. Forrest and Stuart were good cavalry commanders, but Forrest never prevented the Union army from doing anything it wanted to, even thouhg he embarassed them time and again. Stuart was an adequate cavalry commander, but he first failed against the Union cavalry during the Gettysburg campaign and never regained the initiative until he died. Cleburn and Gordon were division commanders for the most part. Neither one served in an independent command. They were as good or as bad as their army commanders. The Union had division commanders as good.
Lee in Virginia was unwilling to reinforce the Army of Tennessee, so it'd have taken a superior in overall command to detach and send corps west to help Bragg.
They also needed someone who could get those Texas troops (25,000 of them sat out the war in Texas) across the Mississippi to bear down on Grant in the West. A corps from Texas and two from Virginia (instead of the Pennsylvania campaign), and they'd have whipped Grant and Sherman and busted the Anaconda by keeping open the road to Mexico.
Lee was at least second-best, and he'd have had to stay in Virginia with Jackson and Stuart, so they'd have been the "A" team in the CSA no matter how you slice it.
Bedford Forrest for overall command in the West, and the force of personality to bring Kirby Smith to heel. He was probably number three or four in the whole pile.
And he could have retired a bunch of those Western Theater generals -- Polk, Bragg, Pemberton, Joe Johnston -- while he was at it. Pat Cleburne could have replaced Polk as corps commander, he was good people, but I don't think he was in a position, having read his c.v. somewhere, to make much of an impression before Chickamauga and Missionary Ridge.