The best weapons for performing headshots are the Liberator (human rifle), Opressor (alien rifle) or the Reclaimer (sniper rifle). Compared to many games, headshots are pretty easy to get in Dark Void.
Take your time to line up the shots, and if you're not using the sniper rifle, it will help if you fire in small bursts so that the recoil doesn't ruin your aim.
I aimed for the head on almost every enemy I encountered and the achievement unlocked for me during chapter 1 part IV.