I've been experimenting with maximizing my weapons damage output because the standard weapons aren't effective in dealing with enemies.

With a rifle energy weapon, the best I am to do is 50.

A pistol style weapon is 30.

Miniguns are the most disappointing of all, 9-12.

I'm uncertain how melee weapons can be modded, I haven't got the ability to do that at this time.

I'm concerned that as my level increases, the enemies I'm facing will also increase in level and therefore, my weapons will become less effective as time goes on.

I don't want to be in a firefight where I am just plinking away for a long time at the enemy health bar because the weapon doesn't do enough damage.

Oddly, they don't seem to have that problem, for some reason, I take a lot of damage.

Are there any ways to increase weapon damage that aren't related to crafting?

Perks

Yep. Perks. There are three dealing with weapon damage.... For rifles, pistols, and automatic weapons respectively. They give nice damage bonuses.......

Heavy and melee weapons too

One thing to keep in mind, there is the damage each shot does, then there is the damage over time from all the shots. So, the Minigun has a much higher damage output over time than a single shot weapon with the same damage per shot as you can't fire it as fast. So, rate of fire has an impact on this.

I know you said not to do with crafting...but the gun nut perk and science perks allow for better receivers on ballistic weapons, and better barrels on energy weapons, that increase damage significantly..

Note that you will find moded weapons and you can remove mods from one weapon and attach to another of the same type. Yes you will have to make the default mod as replacement but this can be done without perks
This is very nice if you get an legendary weapon

This is true...I used that to get a silencer for a gun once..but it becomes tedious work at times for me, so I just maxed out gun nut and science and not worry about it..

Also the luck perk that makes people blow up( can't think of name) gives you an extra 15% damage at rank 3.

The perk is Bloody Mess.
I won't be using that one because I don't like the, well, mess it creates.

I have already maxed Gun Nut and Science, so there is no more advantages to be gained from crafting.
Hence why I specified not to discuss it.

The answer is rly simple its perks, plenty of ways to increase dmg of your wepons/attacks trough perks.(Also if you rly dont want to invest into crafting you can always take out mods out of found weapons and put em in yours if they are better than what you already have)

For example rifle wud need rifleman perk atm my plazma rifle does 60 energy/60 balistic dmg and i havent jet maxed eather crafting(misisng 1 perk) or rifleman(missing 2 perks) also another way that can add to that is finding a legendary weapon with nice bonus like(added 50 radiation dmg, duble dmg etc.. plenty of good ones around)

If that's the case, you may just need to start farming legendary weapons for the extra bonus. There are some good farming guides if you google "fallout 4 legendary farming."

They'll mostly be specialized (+25% damage to ghouls, +50% damage to limbs,) but I have a few good ones that are generic. (Like "violent" weapons that are +25% damage to everything, but have higher recoil. Since I have them in a scoped sniper rifle and a combat shotgun, that becomes irrelevant.

Add in the high level Gun Nut mods and the damage increasing perks and you'll be doing the maximum damage possible.

Getting criticals more often increases your overall dps, you need a high luck for that. Also, there is the perk witch increases critical damage.

Also the damage multiplier from sneak mode if you are playing stealth.

Just because you start a topic doesn't mean someone can't give advice that is related to the topic for others that may be reading and wondering the same thing, especially since the gun nut and science perks are probably the less obvious perks for increasing weapon damage..whereas gunslinger, rifleman, iron fist, big leagues, heavy gunner, and commando are quite obvious that they increase damage..and being lvl 40ish to max out science and not notice the other obvious damage boosting perks? SMH..

Perks that help:

Rifleman: Bolt action and semi-automatic rifles. Ballistic, Laser and Plasma. Up to double damage and 30% armour piercing.

Commando: Automatic pistols and rifles. Ballistic, Laser, Plasma and Gamma(radioactive). Up to double damage and staggers target.

Gun Slinger: Bolt action and semi-automatic pistols. Ballistic, Laser, Plasma and Gamma(radioactive). Up to double damage and cripples limbs.

Heavy Gunner: All heavy weapons, Minigun, Rocket Launcher, Fatman, Gattling Laser, etc. Up to double damage, increased hip fire accuracy and chance to stagger.

Demolition Expert: Up to double explosive damage so Rocket Launcher and legendary Explosive weapons. I think the Fat Man has an explosive component too.

Nuclear Physicist: Up to double radiation damage. Legendary radioactive weapons, Fat Man, Gamma guns, etc.

Concentrated Fire: Up to +20% damage to the same part shot at in V.A.T.S.

Lady Killer/Black Widow: Up to +15% damage to opposite gender.

Lone Wanderer: Up to +25% damage when with no companion. Dogmeat currently doesn't count as a companion so you get the boost with Dogmeat.

Mr Sandman: +50% Sneak damage with suppressed weapons.

Ninja: Sneak attacks with ranged weapons can be raised to x3.5 rather than the normal x2.

Gun Fu: Does +25% damage to 2nd target, +50% to 3rd target and instant crits to 4th target and beyond in V.A.T.S.

Bloody Mess: Up to +15% damage.

Better Criticals: Up to x2.5 damage with crits.

I think that's about it.