The best overall Japanese plane had to be the Ki-84-Ib.
Its only weakness was altitude performance. I think I would disagree with RedTail that it had poor acceleratin performance and bad guns. In fact, the HO-5 cannon are second only to the hispanos used by the Americans and British. Far superior to the Type 99's used by the Japanese Navy, the Soviet Shvak/B20's, or the German 20's. And with 100 octane fuel (very rare to nonexistent for the Japanese late in the war) in post war testing in the US, a Ki84 outperformed a P-51 and a P-47 in head to head testing.
Probably the second best was the N1K2-J that we already have.
The Ki-43 and all the A6M series were both just way too slow, lacked sufficent armament, and had little to no pilot/critical system protection such as self sealing tanks.
The Ki-61 was a decent plane, but overall was only moderately effective against its contemporaries. The Ki-44 would fall into the same category.
The Ki-100 was definitely not as effective as the myth that has grown up around in online sims, as the greatest Japanese fighter. The Ki-100, was a Ki-61-II airframe that used a radial engine, due to the allies bombing the plant that manufactured the engine used in the Ki-61-II. It was actually inferior in performance to the Ki-61-II. Its one saving grace was that the radial engine was simple to maintain and reliable in a time when spare parts, quality maintenance crews, and good quality fuel was a rarity in the Japanese forces. While it was a good turning aircraft, it was quite slow.