I have an idea for what my players can do once they’re finished with Barovia. I’m thinking they find their way through the mists to another domain of dread set in a small cliffside harbour village. The village has a few problems at the moment. One is that a gang of wererats have infested the sewer system beneath the village. Another is the strange disappearances of fishermen caused by kuo-toa. The kuo-toa have been kidnapping people to use as offerings to their god, a lighthouse that overlooks the harbour at the top of the cliff. The god is yet to be truly born. 
My question is who should be the darklord of this domain?

I’m thinking either the high priest of the kuo-toa or the leader of the were-rat gang. Other options are the god itself, somebody in a position of power in the village (mayor, etc.), or somebody else. 

I should also mention I’m planning on having the carnival domain from Van Richten’s Guide make a stop at this village. 

This is only early stages of planning. They’re about halfway through Curse of Strahd at the moment. 

It's usually easier to come up with a Darklord first, and then design the domain around their particular personality, powers, aesthetic etc.

However... right now the pieces you have suggest a domain of deception. Wererats hide underground and blend in with 'normal' society. The kuo-toa also have strong ties to the underdark and instead of worshipping gods of their own invention, they're somehow fixated on this lighthouse. Little is as it seems.

One option would be to have a public "Lord" who seems menacing but is not actually the true Darklord, with the Darklord instead hiding in plain sight so they can more easily manipulate the pieces on their personal chessboard. A Machiavelli or Moriarty-like figure at the center of a web. You could even lean right into that metaphor and make them a drow, whose schemes drove an entire underdark city to tear itself apart before the Dark Powers took them. Have the sun basically never come out, so creatures that don't like the sun can move around freely for the most part, but the Darklord themselves might have their movements restricted in another way to torment them. The kuo-toa's fear is what's driven them to worship the one source of consistent illumination in this dark realm.

In that kind of scenario, I'd add in even more factions of "monsters" in the village who may or may not be willing to work with the party. Just have constantly shifting alliances and feuds, so the PCs never quite know who they can trust or even ally with towards a short-term goal, even though that might be their only way out. Basically put the settings of Red Harvest/Yojimbo/Fistful of Dollars and The Prisoner in a blender.

Just to throw out an alternate idea, I would consider making the lighthouse keeper the actual Darklord of this domain. The wererats and kuo-toa are obvious threats to this cliffside harbor village, but it's the reclusive hermit that maintains the shining beacon on top of the cliff that is the truly monstrous being. Perhaps, they control and direct these monsters akin to the Moriarty-like figure that AntonSirius mentions above. Or maybe this Darklord wants to "protect" the villager and its citizens from the "hidden evils" no matter what the cost...

How many "suspicious ships" were allowed to crash into the rocks to prevent travelers from foreign lands to arrive? What other types of defenses have been created besides the lighthouse? And what are the consequences of these changes? For example, the wererats might be the invasive species that overtook sewer system when the lighthouse keeper let them loose to drive away a previous threat. 

And why do the kuo-toa sacrifce captives to the lighthouse? Maybe because they sense the touch of the Dark Powers upon the building, and they mistake this dark energy as divinity. And maybe they do it because it frustrates the Dark Lord, who wants to protect his village and loses more citizens because of the lighthouse that is needed to protect the fishing boats.

I agree with what was previously said about making the Darklord before the domain itself. The whole of the domain was created around the Darklord to serve as their own personal torment. What would be this Darklords relationship with the Kuo-toa? Were they part of the Darklord's life before they became a Darklord? Is this another creature who used to live in the underdark? Maybe they manipulated the local Kuo-toa into seeing them as a god, and therefor attempting to become one? Could be anything from a drow to a duergar really. Manipulated the Kuo-toa into doing horrible things could have been enough to get the attention of the Dark Powers. 

It does depend what theme of horror you seek to make? From what I gather this sound much like it could be Folk Horror combined with something like body horror or cosmic horror depending on how much weirdness you want to add. With the whole Kuo-toa cult it does feel similar to something Lovecraft might have writen with his deep ones. An isolated fishing community of fish people who regularly sacrifice victims to their thing inside the lighthouse. 

I like what you've got going here. 

These are all great ideas. 
I’ve decided to add a few more things to the cliffs. 
A bronze dragon dwells in a network of cliffside caves along with a colony of kobolds who serve him. I like the idea of drow living here. I am thinking the darklord could be a parasitic fungus that has infested most of the major players in the town (I.e the boss rat, the dragon, the lighthouse keeper, the head drow priestess). The fungus’ goals are simple: multiply and expand. 
The kuo-toa are basically the downtrodden underlings and slaves of the factions above and are seeking freedom. The awakening of their god is the way out for them. 
I think body horror and cosmic horror are the routes I want to take. 
The disappearances and kidnappings are coming from all sides. 
The wererats mostly steal food to give to their enormous, grotesque leader, infested with the parasitic mushrooms that compel it to consume more and more, resorting to cannibalism when food runs short. 
The dragon has lived here for ages and likes to keep order throughout its town. A kuo-toa uprising would bother it greatly. The dragon has recently been infected by the fungus and uses its minions to spread it further as well as its usual goals of keeping order on the cliffside. 
The drow came up from underground when the kobolds’ mines went too deep. They have taken a liking to the cliffside harbour, with the sea fog and frequent storms blocking out the sun so they can live there comfortably. They take “donations” from villagers and travellers and use the riches as offerings to Lolth (I’m not sure if Lolth is interested in gold, I’m not very well versed in drow lore if I’m being honest). They give gems to the dragon as a kind of tax. The village itself gets its livelihood from fishermen who brave the dangerous surrounding ocean, and from hunting crabs on the nearby mudflats where the escaped kuo-toa reside. 
The dock rarely has ships stopping in but they are a welcome source of trading when they do. 
The domain was created when the fungus first took over the head rat. 
The fungus needs hosts to reproduce so draws travellers in through the mists hoping to take them. 

Thank you all for the feedback. I’m hoping to hear some more :)

Another option is the captain of the sailors. He made landing here and has been stuck by the sea-fog for about a week.

Perhaps this is his domain and the dark powers are punishing him for being an underhanded, thieving pirate rather than the tradesman I was picturing.

I think this makes more sense than the fungus, although I do still like that idea.

Quote from Cuplaser >>

I am thinking the darklord could be a parasitic fungus that has infested most of the major players in the town (I.e the boss rat, the dragon, the lighthouse keeper, the head drow priestess). The fungus’ goals are simple: multiply and expand.

So if this is some sort of cosmic intelligent fungus, that could potentially work. It wants to expand, needs to expand, but it's trapped in this tiny little fishing village and has nowhere else to go. Maybe it allows outsiders into its Domain so it can infect them, or at worst in the hopes that they can "cure" some of those it's already infected, just so it can infect them again later and maintain the illusion of expansion.

Remember that the primary purpose of a Domain of Dread isn't to provide adventurers with quests. It's to torment the Darklord it contains. The party is just blundering into the middle of it. Once they leave, things will be eventually reset back to where they were. There's no "winning" for the players here, no defeating the BBEG and saving the day... only horror and (maybe) escape.

Yes I was definitely thinking that the fungus was sentient. I love your interpretation of it.

Love the sentient fungus idea, and I wonder if the fungus (and its ultimate lair) could be based on something around this:

• The fungus is trapped in a network of natural caverns in the cliffs below the lighthouse
• Its ultimate goal is to escape the lair and continue to spread, but the domain of dread exists to torment it: the fungus cannot expand beyond the borders of the domain, and even there, some kind of special weather feature regularly kills off the spread (regular wildfires? constant rising plagues that affect the fresh growths of fungus, driving it back, but also afflicting the populace with horrific mutations)
• The lighthouse is actually a trap - like a wrecker, it actually works to draw in light rather than give it, which causes travellers in the astral plane to appear wrecked on the coast. It would be a 'darkhouse' essentially. The fungus lures them in to infest them, in the hope that such travellers might carry its spores away into other planes of existence, freeing it - but such attempts are futile. When an infected traveller tries to leave, the fungus mutates them into gibbering mouthers or other aberrations. The fungus doesn't know this, and believes that it can succeed one day
• The infested humanoids suffer tormenting dreams that require them to carry the spores into the mist, ultimately destroying themselves
• The mists only part when the sentient fungus is destroyed. But when it is purged from the land, its killer (invariably a powerful adventurer) becomes secretly infested. Unknowingly the adventuer then leaves the domain of dread , and infests part of another realm or material plane. The fungus develops, consumes the creature and has them build a lighthouse atop a cliff. Over time, as the fungus regains its old power, this new land begins to change, even the cliffs, until it has reshaped itself into the Domain of Dread and the mists descend once more...

I just realized, at least unconsciously on my part, that this is a bit of a riff on Richard Stanley's film version of Color Out of Space, but that's not at all a bad thing

Quote from AntonSirius >>

I just realized, at least unconsciously on my part, that this is a bit of a riff on Richard Stanley's film version of Color Out of Space, but that's not at all a bad thing

 Seems like an interesting film and it's exactly the kind of horror I'm looking to emulate.

I have a map that I drew of the bay

Quote from Sanvael >>

Love the sentient fungus idea, and I wonder if the fungus (and its ultimate lair) could be based on something around this:

• The fungus is trapped in a network of natural caverns in the cliffs below the lighthouse
• Its ultimate goal is to escape the lair and continue to spread, but the domain of dread exists to torment it: the fungus cannot expand beyond the borders of the domain, and even there, some kind of special weather feature regularly kills off the spread (regular wildfires? constant rising plagues that affect the fresh growths of fungus, driving it back, but also afflicting the populace with horrific mutations)
• The lighthouse is actually a trap - like a wrecker, it actually works to draw in light rather than give it, which causes travellers in the astral plane to appear wrecked on the coast. It would be a 'darkhouse' essentially. The fungus lures them in to infest them, in the hope that such travellers might carry its spores away into other planes of existence, freeing it - but such attempts are futile. When an infected traveller tries to leave, the fungus mutates them into gibbering mouthers or other aberrations. The fungus doesn't know this, and believes that it can succeed one day
• The infested humanoids suffer tormenting dreams that require them to carry the spores into the mist, ultimately destroying themselves
• The mists only part when the sentient fungus is destroyed. But when it is purged from the land, its killer (invariably a powerful adventurer) becomes secretly infested. Unknowingly the adventuer then leaves the domain of dread , and infests part of another realm or material plane. The fungus develops, consumes the creature and has them build a lighthouse atop a cliff. Over time, as the fungus regains its old power, this new land begins to change, even the cliffs, until it has reshaped itself into the Domain of Dread and the mists descend once more...

This is very cool. I will probably take inspiration from here.