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Out of every single weapon, I find myself using rifles more than anything, the Anti-Material rifle is the best weapon in the game for me, hands down. Taking Death Claws down with a sneak 1hko head shot from half a mile away is just too good to pass up. I prefer SMGs or Mini gun vs stuff that doesn't have crazy health and armor, the Mini Gun with AP ammo lets me mow down 5 Cazadors without getting hit. I think the modded mini-gun is actually better than the avenger, because it lets you keep 2x more ammo in the magazine, vs 5 Cazadors, that extra 120 rounds in the magazine is life and death. So basically, at end game, I'm either using the Anti-Material rifle, or modded Minigun, if one doesn't work, the other certainly will. The minigun does suck vs super mutants and death claws, even with AP ammo, which is where the Anti-material rifle comes in.
I wasn't impressed with any of the explosives or energy weapons, guns seem to rule in this game
"Best" is subjective, but if the criteria is that I could only carry exactly one weapon? I'd say that a carbon fiber sniper rifle with suppressor is the most useful weapon in the vast majority of fights in the game so that's what I'd choose.
Using it makes the game too easy though, so for actually playing for fun rather than trying to trivialize every single encounter from a mile away, my favorite is the Ranger Sequoia with a Cowboy build.
Modded sniper is only better for SNIPING since it's silent.
Gobi has 1/2 AP cost of regular sniper per shot. Also much higher rate of fire. You can dominate with it in vats and non-vats. I only carry modified sniper rifle so I can sneak attack silently.
Keep in mind however that there are caves and buildings where sneak attacks are too hard to perform (enemies looking in your direction when entering room -> no sneak hits). That's where you draw Gobi and kill everything.