Maj. Gen. John C. Breckinridge. Despite being mostly a political general, Breckinridge did pretty well in the west with the AoT, as well as in the east at Cold Harbor and with Early in the Shenandoah.
Edit: I'd also nominate Trans-Miss. Texas cavalry commander
Maj. Gen. Thomas Green. Definitely one of the most underrated cavalrymen of the war. He was largely responsible for the Confederate victories at Valverde (in the NM Campaign) and Galveston Bay. In the latter Green led a contingent of his Texas cavalrymen aboard the cotton clad steamer CS
Bayou City, capturing the USS
Harriet Lane and almost singlehandedly winning the battle. "Horse Marines", they were called after that. Yeah, he was that awesome.
Green went on to command the Sibley Brigade in Louisiana, later taking command of a small cavalry division and later a cavalry corps while serving under Richard Taylor. His Texans fought in a number of actions that go unknown to most today, including the the Bayou Teche Campaign, Texas Overland Campaign, and Red River Campaign. Unfortunately his reckless daring got him killed at Blair's Landing in the latter; like Green always lived, he died in the thick of the fight. Green was beloved by his Texans, and not just his horsemen but he was well known through all Texas at the time. He had quite the life before the war as well, having fought at San Jacinto, was active in Texas politics, served as a Texas Ranger, and fought in the Mexican War. All in all, he lived and died a Texan. So yeah, why anyone hasn't written a biography on Tom Green is beyond me.