You're not
supposed to kill Boba Fett. God forbid he dies and angers all the Fett fans out there...even though he was
supposed to die in ROTJ.
*Runs from Fett fans*
Anyway, you just want to hurt Fett enough that he flies away for a bit and gives you some time to destroy the weapon crates. He's invincible anyway. He's a nusiance, but really not as tough as I would have thought he would have been. Just be careful when he whips out his rocket launcher and push the homing rockets away from you.
spoiler:After you destroy the weapons crates you'll have a final showdown with him by your ship. If you win, Boba taunts you in an attempt to salvage his wounded pride and flies away.