Ooh, tough choice. I hate the boss fight here, but the design inside of Leviathan was pretty cool. Disgusting beyond belief....but really well done.
Most of the environments are pretty cool, in fact. I'd have to say my favourite area is Nevan's lair; not just where you fight her, but the damp cavern leading to it. The design is actually quite beautiful, especially when you go into that one side chamber that's lit with many glowing minerals in the ceiling and walls-and the air too, apparently. I'm not sure what makes it glow, really, but it reminds me of swirling galaxies, there.