I did use the search the function and couldn't find an answer to this. I think I'm pretty much screwed: Playing the game for the first time and absolutely loving it. Must've at least put in 15-20 hours in already.
Anyway, today, I finally went to the Necropolis, and can't get the water chip quest from the ghoul leader, because when I went down in the sewer, he, and everyone else, was already dead. Does this mean that I pretty have to start over if I want to continue with the game?
It seems that you've arrived a bit late in the game. All the ghouls are dead, because supermutants killed them. You aren't screwed however, you can still find the chip there.
Yes, you can simply get the chip and bring it to your Vault, you don't need to do the quest. You can't do it anyway now that the ghouls are dead, at least I do not know if there are any other quests related to the chip in Necropolis