It's been a while since I've played the game, so I apologize for any vagueness on my part. But if I remember correctly, the crate is suspended in the air by some kind of crane or similar thing. Before you start the fight with the bounty hunter, take that one female party member that uses a wrench for a weapon and go to the crane-like device. You should be able to click on the device and wrench-girl should do something to it. I think, after that, the crate lowers to the ground. You can then start the fight and you should just be able to shoot the crate.

Again, sorry if that's a little vague.