So I had a chance tonight in a game on vassal to use crackshot against an evade added from a bomb obstruction on my opponent's ship.

He claimed that the evade came after I wanted to use crackshot, so I couldn't use it. I didn't see how, as it's an added result just like reinforce which can be cracked.

Am I mistaken? I didn't want to argue with him as I was losing badly already and just wanted the game to end.

You are correct. Nym's ability is a dice modification, which (unless otherwise stated) happens in the appropriate "Modify Dice" step, which is long before Crack Shot goes off in "Compare Results".