It was actually easier to kill the Shadow Snake than two of the three Shoggoths he killed. One got loose in a lab I was exploring, ate some stuff, and split into two. I didn’t want to run back up to the surface to get heavier firepower lest they get further out where there were piles of stuff to eat, so I decided I had to kill them here and now.
I managed to close a door on the second one, and then had a couple of false starts that ate a ton of ammo, because it would heal all the way up whenever I had to stop to reload. Luckily I had picked up a bunch from armories. I quickly figured out I had to get the bastard pinned into a corner with the help of my two NPC buddies (a mutant and a dude in plate armor), wail on it repeatedly in melee and wait for a moment when its HP went into the yellow, then unload my modded RM99 revolver’s six shots of 8x40mm HVP ammo into it, to finish it off.
Then I could stop to reload, and go into the other room and kill the other in the same laborious manner, which thankfully had stayed near the door (probably attracted by the sound?) rather than going to the other end of the room and getting out.