My rankings from best to worse are based on their respective performances as Corps and/or Army commanders.
1. Hardee
2. Beauregard
3. Bragg
4. Hood
5. Polk
Hardee, known as "Old Reliable" was a solid, but not spectacular commander, who had the admiration of his troops. His tenure with the AoT cannot be separated from that army's generally unsuccessful record throughout the war, but Hardee's flank attack at Stones River almost brought the AoT a victory in that encounter.
Beauregard oversaw a number of high points in Confederate military operations, from the assault on Ft. Sumter, the routing of Union forces at 1st Bull Run, the defense of Charleston in 1863, and the successful attempt to prevent Petersburg from falling into Union hands in June 1864. At the same time, his personal difficulties with Jefferson Davis, and his often unrealistic strategic plans put a damper on his overall command abilities.
Bragg's irritable personality led to ongoing fractures with his senior command. His command of the AoT was marked by mostly defeat and withdrawal, and his inability to properly size up his opponent and understand battlefield conditions led to disappointing results at Perryville, Stones River, and Chattanooga.
Hood was a highly capable division commander but higher command was not his forte. His overly aggressive style was something of a rote approach to warfare, but that only led to disasters at Atlanta and Franklin. His habit of blaming subordinates and even his own rank and file for a perceived lack of "aggressiveness" did him no favors.
Without his friendship with Davis, Polk would likely not have attained army command. He practically lost the war for the Confederacy by his ill conceived occupation of Columbus, Kentucky in September 1861, which tilted that state away from neutrality. His disregard for effectuating Bragg's orders before and at Chickamauga harmed the AoT's opportunities for degrading the AotT in a meaningful way.