Q:

What is the most powerful semi automatic non legendary weapon with all the perks?

What is the most powerful single shot non explosive and non legendary weapon in the Fallout 4 vanilla game with these requirements:

You have all the perks (including the companion perks).
You have all the best mods.
You have all the best armors (+stat - perception armors).
No companions with you.
No drugs.
Hidden and stealth active.
Rifle is preferable but a pistol will also do.

I am asking this question due to me being over level 100 already and just want a 1 shot weapon although at this level some super mutants wont go down even if you critical shot them in the head with an instigating .50 cal weapon.

A:

I would say a Gauss Rifle with either the Two Shot perk or the Instigating perk on the gun, the best mods, and the correct perks would be the most powerful semiautomatic weapon in the game. The Wiki seems to back this claim:

The Two-shot legendary variant of the Gauss rifle is arguably the most powerful rifle in the game. With the right perks and the right circumstances this weapon can kill even the strongest enemies in a single shot.

The 6 crank laser musket is the only thing that beats it, but under proper circumstances, it's still more powerful. According to the Wiki:

However when stealth combat is involved, and a silencer is equipped; with the Mister Sandman perk 50% more sneak critical damage is dealt. A fully upgraded Gauss rifle along with a fully upgraded Ninja perk will boost the sneak critical to 5.25x the base damage (6.3x with Deacon's Cloak and Dagger perk). One can combine that with Rifleman 5 and can do approximately 2000+ ballistic damage. (As of patch 1.4 the maximum multiplier is 4.8) One of the highest amounts of single shot damage. During a field test with the 6-crank laser musket at its highest, the laser musket does not do as much damage as a fully upgraded and perk supported Gauss rifle.

Given all this, I would argue that this is the most powerful semiautomatic rifle you can use with the appropriate perks. Even without the legendary perks, they are still a viable option. Although you need to charge up each shot to get maximum damage, if you use VATS, the shot is automatically charged and skips having to wait to charge it up (according to the Wiki).

A:

You said no legendaries, so Timmy Tim's answer is probably correct, but if you dropped the legendary requirement then you could get enough damage to kill anything in one shot, assuming you don't mind standing around and getting ready for a while.
A Neverending Laser Musket can do an arbitrarily large amount of damage if you crank it long enough.
Per Nukapedia:

as the musket uses its "clip" to store the crank charge, and this mod sets the clip size to the amount of ammo in your inventory, the mod effectively removes the crank limit. Since the damage of the weapon is based on how many cranks you can give it, this gives that single shot a devastating amount of damage. For example, at 200 cranks, a single shot can do about 30,000 damage.

