My nomination for the greatest military aircraft of the past 100 years is the same as for the greatest civil aircraft: the Douglas DC-3, in this case in its C-47 military derivative.
Why not a fighter or a bomber? Why a lowly transport? Consider:
Think about it. You can take any fighter or bomber aircraft you care to mention in the last half-century. Try operating a squadron, or a wing, or a group of them anywhere in the world without the support of dedicated air transport facilities. How long would they remain in operation? Not very long . . . and it's the C-47 and its successors that make such facilities possible, and thereby allow the rest of any Air Force to remain in operation.
Hence, I nominate the C-47 as the greatest military aircraft of the past 100 years.