The best way to finish this mission is by using Evan's Repeater, as it has such a huge magazine. Go into Dead Eye mode and paint as many crows as you can. Make sure you stand some distance away so you can get them all. Afterwards, just keep shooting them. Using the pump shotgun and shooting the crows right before they enter the silo works really well, it might take a couple of tries though.
Another way is to only shoot the crows you see swooping in. Whenever you see a crow who's wings are arched (like this: ^*^) use deadeye to paint it. it will let you get most of them and you save a ton of ammo. Pump or Semi-Auto Shotguns work best or you can just chuck dynamite up on the silo roof.