Top-tier weapons seem to be
Rifleman = Gauss Rifle or Plasma Sniper. Gauss Rifle works better if you are sneaky snipermans and want to use a silencer. Plasma works better if you just want to spam a fuckton of VATS shots into people.
Automatics = Automatic Combat Shotgun or Assault Rifle. CHOOM CHOOM CHOOM HERE COMES THE DEATH TRAIN. Assault Rifle works better if you just want one gun to do everything with, though.
Gunslinger = Plasma Pistol. There's an easter-egg gun you can also get that is decent but the Plasma Pistol is still king. There's a unique (as in, it also has its own unique model too) silenced 10mm you get during a certain faction's story that may work better for you if you're going 100% stealth crits.
Unarmed = Deathclaw Gauntlet or souped up power-armor punches.
Melee = Super Sledge or Combat Knife. I just fucking shanked a Deathclaw in two stabs with a Combat Knife because of Ninja perk. 10x damage on a weapon that also does bonus damage on stealth crits is no-fuckin'-joke.
Explosives = Who the fuck plays a dedicated explosives build come on. Go make Plasma Grenades and kill your companion characters and yourself constantly sounds like a great time.
Stealth + Ninja is fucking god-tier though. Clear out entire vaults full of assholes butt-naked with a combat knife. Kill giant beasts with just a blade and no fucks.