As Sniper likes to say: "The best tool against a sniper is another sniper". It is not a rare case in combat, but you have to keep in mind that the enemy is a well-trained and well-prepared shooter. They are smart, will take up tricky positions, and try to deceive you. Even if they're not a professional military man, but a former gamekeeper or so. You need to "tie down" the enemy sniper, make them show themself - then, they're all yours. Well, these are recommendations I was asked to give you. Scavs just find rifles with scopes and climb up on the roofs or rocks, thinking they're actual snipers. Those are the ones you have to eliminate.
Generally, Customs is the best location to kill sniper scavs as it has the most. Killing them at night for this quest is recommended as you can quickly run down the main road through the map to see all of them under the cover of darkness. In order from left to right:
1. Construction Sniper. Spawns extremely frequently.
2. Vacuum distillation tower. Spawns uncommonly.
3. Warehouse Rooftop Sniper. Spawns about half the time.
4. Checkpoint Sniper. Spawns about half the time.
5. Sniper on rocks above Scav checkpoint. Spawns uncommonly.