Just shoot the little poppers when you see them. One pop will kill a few of them each time. They also rupture when they hit your shield. so getting 100 should be no problem by the end of the level.
The easiest way to get this is while beneath the ship, you will come to a cliff-side where there will be hunters fighting Carrier flood forms. Don't drop down, but instead stay up top and the carriers continue to spawn. With the Bandanna skull, they will continue to spawn and you can just continue to grenade them until you get the achievement.