I'd say the most objectively creepy of the ones you listed is a tie between the Lakebed Temple and Arbiter's Grounds.
Arbiter's Grounds is clearly TP's "scary dungeon", so while it's creepy there's not a ton that can be said about it. It has the standard undead theme and plays off it the entire time. I was fond of how it mimicked a tomb, because it helped sell the undead theme more than usual. That said, I think it suffered from some elements of weak atmosphere and while it was pretty creepy most of the time, something about it never became truly scary, like say the Bottom of the Well in Ocarina of Time. Because of that I think it ties with the Lakebed Temple.
Now the Lakebed Temple, anyone who knows me well enough will realize that I have a specific fear that's a sort of underwater claustrophobia. Considering that the Lakebed Temple is at the bottom of a huge lake, and takes place in this underwater cave network, it definitely preys on that fear. That said, even objectively, I think the dungeon has a disturbing atmosphere. A major component of this was the music, which was just eerie. Arbiter's Grounds' song was creepy too, but it wasn't subtle. To use an analogy, it was kind of like if something jumped out at you to scare you rather than if they manipulate your emotions and tension. Arbiter's Grounds was explicitly creepy, but Lakebed Temple was more implicit I thought. The deeps are always supposed to contain intold horrors, and I think the culmination of the battles against the Deku Toad and Morpheel really helped accomplish that.
There was just enough sections of the Lakebed Temple that feel eerie. You're isolated. You're underneath everyone and everything. There's no one else down there and no one will be coming. You're alone, with nothing but the darkness and water. That's how I see the Lakebed Temple.
Palace of Twilight was also creepy, though it isn't on the list. Some of the interior sections were eerie and the Zant's Hands were kinda nerve wracking, but I think the worst part is outside the palace and on the balcony, where there's just this void of sky beneath you. It's far more disturbing than the City in the Sky, because you don't know what it
is. It's just nothingness. Freaks me out. Of course there's also the creepy moaning Twili guys.
But I don't think it's as bad as the Lakebed Temple.
Also, if you look at the paintings on the walls they're of this creepy guy >.>
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