I really don't think you can separate the political and military leadership and judge them separately in this kind of debate. Hitler, Stalin, and FDR were all the commanders-in-chief of their respective militaries. In which case FDR was easily the best, because he interfered in matters he did not understand the least.
Overall I would say the US. The US easily had the best admirals of the war. Admirals Nimitz, Halsey, King, et al did a fantastic job defeating the naval forces of the Axis nations and ensuring that the US could get supplies and troops where they needed to go. This was instrumental to the Allied war effort and could not have been completed without them.
Yamamoto had the problem of constructing large set piece operations where none of the various pieces could support each other. If there had been BB and CA anti-aircraft guns defending the carriers at Midway it would have been a different story, but instead they were 600 miles away.
I'd say the best overall ground commander was Zhukov. He was crucial to defending all three cities (Leningrad, Moscow, and Stalingrad) and without him the Soviet Union would have likely crumbled in late '41. He was then very successful on the offensive.
Rommel had the problem of never seeing the grand strategy of what he was doing. Sure he could win in North Africa, but his constant demands for troops that could be better used elsewhere show a commander who should have not been sent to backwater fronts where you will always get second rate equipment and troops. Frankly North Africa wasn't that important and Germany never should have sent many troops there, focusing more on the Soviet Union. To me Guderian and Von Manstein were better overall commanders. Guderian invented modern blitzkrieg after all.