So, I am not really clear on whether or not the Op has managed to solve his problem yet.
If not, here are a couple of things to consider:
1: Altering the behavior of npc's dependent on player activity is not a form of singling out a given player. The bad guys, unless their stats say otherwise, should be at least as intelligent as the player characters. No good group of baddies is going to leave a high powered ranged character alone. You dont have to rebuild your encounter to take care of this, just modify the behavior of the creatures and baddies in your encounter to take advantage of player oversights. In otherwise, be more battlefield aware.
2. If he is playing a sniper, note I am not sure he is. Modify his play style, a sniper should shoot, then move and hide, not be taking tons of attack actions in one round. If he takes more than one shot, force him to be stationary. Paint a target on his back so to speak, for using bad tactics. I dont know what all the feats he is using are, and I dont really care, the whole reason you allowed this in the first place was for flavor. If he isnt maintaining his flavor profile, then he shouldnt get to keep all the perks.
3. For the love of god, partial and full cover are your friend, as are any other factors which create miss chance 20% is good, 50% is better. Have your spell slingers take cover and take aim at the glass cannon.
4. Dont nerf his gun... As both a player and a game master, I understand the importance of having fun with what your playing. The more you can modify the game to be both challenging and fun, without directly interfering in the characters, or players, the better. In other words, if you need a control mechanism, focus on the invisible mechanics that the players dont get to see in action.
For instance, it is not unreasonable if he is taking multiple shots in a round, for you to add a five, or ten percent miss chance for each successive hit in a sequence. The term that covers this in terms of firearm physics is called cumulative recoil. Each shot becomes harder to maintain on target for each successive successful shot. Reset the miss chance when he misses. This you can do, without ever telling him what is going on, you can manage miss chance with a subtle dice roll, which you dont have to disclose.
Honestly, given everything else that has been said, I think you are struggling with the ability to interpret the rules and modify them fluidly where they concern your job as the dm. To that end, I recommend research. Look into the core combat mechanics, how they work, and how you can interpret them to be appropriate for any given combat situation.
If you dont want to force flexibility on the players at your table, then it is incumbent on you too be flexible instead.