Why does the boss say that the fly is plucky?

Merriam-Webster defines "plucky" as spirited and/or brave. A plucky individual, then, is someone who shows courage and determination in the face of difficulties. The boss sees the fly as plucky because the fly's efforts to clean itself off and survive are unceasing. The boss first notices that the fly has fallen into the ink pot, and the boss rescues the fly. He then watches how the fly begins the laborious task of cleaning itself. Just as the task is nearing completion, the boss decides to begin torturing the fly. He drops an ink blot onto the fly, and the fly once again begins the entire cleaning process over again.

But then, as if painfully, it dragged itself forward. The front legs waved, caught hold, and, more slowly this time, the task began from the beginning.

This is when the boss thinks about the fly's plucky nature. The fly is doomed at this point, but it has a "never say die" attitude about it, and the boss admires that. This attitude in the face of adversity is plucky.

"Plucky" is an old-fashioned word used to describe someone or something that's brave or courageous. In "The Fly," the character of the boss, traumatized at being reminded of his son's death in World War One, seeks to take his mind off things by torturing a fly on his desk. He slowly drops ink on the fly, waiting for it to struggle free before he heaps another drop on top of the little creature.
The boss is impressed by the fly's pluck, by the courage it shows in trying to struggle free despite the blobs of ink raining down. But he continues to torture the fly anyway until, eventually, it dies. The boss may admire the fly for its plucky spirit, but there's simply no way he's prepared to let him go. Engrossed in the fly torture's the boss has momentarily forgotten about the tragic death of his son.