If that sniper has a insane damage, then that sniper might use a 12.7mm sniper rifle.
In that case, you should try Caltrops, especially crawler poison caltrops, Dirty Tom sometimes sell them, and might found in random loot.
Caltrops may prevent the sniper doing anything because he doesn't have metal boots and enough AP for 12.7mm sniper rifle.
And also, you should plant many many bear traps in the warehouse(poisoned is better), you will have a lot of time because if you don't talk to agent Henderson, the assault will not began.
Frag or heat mine are some good option too, since they will not trigger bear traps, 5 or 6 MK II set together may kill them instantly, but you might need 20 or 25 trap skill to do so, try your jacknife and trapper's belt, junk yard surprise.
If you set the warehouse to a good enough deathzone, you don't even need to do anything, the enemy will be dead easily. This mission is already be NERFED.
Morphine shot is good too if you have to take that sniper shot, high frequency shield helps.
Locus of Control+Mental Breakdown is a powerful combo too.
And you have final method, be a save scum because every time the enemy will be changed, even in some pattern no sniper will show up.