What to do against the sniping guards in protected shelters?

Even if you're standing right next to their hideout, I've found that you can't get them with your sword - you have to get them with a ranged weapon. (Apparently Ezio doesn't have the dexterity to stab guards through an open window, or something.) I've had success taking them out with my hidden pistol and with throwing knives. Bombs, while throwable, never seem to work for me, except maybe for obscuring their vision while I line up my shot.