If we are talking the best overall general, in terms of mastering the tactical, strategic and political, I'd say the award goes to Ike, Monty or Slim. However, if we are including Admirals (especially in the Pacific), I'd give it to Nimitz, Spruance and Fletcher at Midway. Up to that point, the IJN was the "French Army of Austerlitz" to the USN: astoundingly victorious throughout the Pacific. In six months, they'd beaten not only the United States Navy, but the legendary Royal Navy as well. The strategic setbacks dealt by the IJN to the USN/RN were probably the largest in their naval histories, in addition to the losses to British and American prestige in military losses to a non-Western power. Its one thing to watch a bunch of crazy Russian sailors in 1904/05 lose to Japan, its different when its the legendary Royal Navy.
Unlike many WWII victories, Midway can be claimed as a solely American victory. It was American intelligence that cracked the Japanese code. It was the American Navy (and Army Air Force) that not only crushed the First Air Fleet, but had to sacrifice many pilots in "distraction" attacks to prevent Nagumo from launching a proper strike. It was also the turning point in the Pacific War, where a string of unmitigated (except for the Coral Sea) Japanese successes were turned into many years of Japanese defeats. While the U.S. Army must take a back seat to efforts by the British and Red Armies in many respects, the American Navy more than carried its own weight in the Pacific, and dealt most of the "Decisive Blows" against the IJN. The Soviet Navy was more than not present: it was in a non-aggression pact with Japan for almost all the war. The RN and Royal Australian Navy played major roles, but were not present at Midway specifically. In one swift stroke, the balance of naval power went from the IJN to the USN in terms of the most important asset: carriers.
Certainly, the Red Army and Soviet Union can claim a lion's share of the blood-credit for defeating Nazi Germany. But the British Empire and United States can claim victory in the Pacific against the greater navy (the IJN would have utterly owned the Kriegsmarine), and what was, in 1941, the best at naval aviation in the world.