Ya know since they are "auto weapons" or are they only affected by the heavy weapon perk?

They are only affected by the heavy weapon perk.

I see. Thanks

It might be worth noting that legendary "Explosive" weapons do have the explosives perk benefits applied to the explosive damage, but that's true generally, not just the miniguns and gatling lasers. Someone seems to mention it whenever this question gets asked, though.

is there a perk that increases energy weapon damage? I know about the radiation damage perk but I'm not sure if that effects energy damage as well.

No, but the Tesla Science! magazines add a perk that increases critical damage with energy weapons. Otherwise, energy weapons are governed by the other perks - so a Laser Rifle is under Rifleman, Automatic Laser Rifle under Commando, and Laser Pistol under Gunslinger.

The Laser and Plasma weapons fall into the same category as the ballistic weapons.

Semi-automatic and single fire rifles - Rifleman

Automatic pistols and rifles - Commando

Semi-automatic and single shot pistols - Gunslinger

Heavy weapons, i.e. Gattling Lasers - Heavy Gunner

Energy and physical damage are only affected by other perks like Lone Wanderer, Bloody Mess, Mr Sandman and Ninja when sneaking and with Suppressors, etc.