There'll always be an argument as to who the greatest general in American history is. Some would argue MacArthur while others will scream for Patton. A few could make an argument for Bobby Lee while some would say it was WT Sherman.
IMHO, the most brilliant general in American history is George C. Marshall. This guy managed to keep such disparate personalities as Mac, Ike, Patton, Bradley, and Clark on the same wave-length without going insane.
Patton and Lee as Field Generals and Marshall and Ike as Organizational Generals
However, Lee filled the role of an organizational General during the early years of the CW. I am not sure which other Generals accomplished both tasks.
I would also scratch Sherman. The actions of his troops on the March to the Sea should have resulted in his Court Martial.