Aim at the Banshee's stomach normally, then scope and take the shot. It's a lot harder to track her erratic charge movement while continuously scoped. But if you're a Salarian Infiltrator you should be Energy Draining instead, and saving the sniper shots for when her barriers are gone.
I've noticed that there are some subtle armoured spots on the Banshee, and a few are on her head. Hitting those points greatly reduce the damage, just like the armour plates on the Brute, but her stomach and buttocks are unprotected so I just aim there.
If you have a Human or Salarian Engineer on your team, and they have Incinerate and Overload/Energy Drain, they can solo the Banshee. If that's what they're doing, you're better off dealing with whatever is trying to interfere with that. Ravagers in particular; kill them on sight.