Boss battles are scarce in custom maps, usually more like arenas against some high tier enemies or just a Chton thrown there, so they are hard to find. You'll find boss battles the most in the second official Expansion, Dissolution of Eternity, than in custom maps.
Amongst those i remember and i can recommend the most ... there is this ones, but beware that some are in packs that are quite hard or on non-solid made maps overall, even if the boss fight is good. The most inventive things in custom maps tend to come in the less polished ones.
Very inventive boss battle.
This is a very good boss battle, but its the only good thing about the map.
The dragon battles in this ones. There is one more but not as good. Beware of the first levels and play on skill 0 or 1.
There is another with a big lava bug that i liked a lot, but i cannot remember where i have seen it. Found it!! https://www.quaddicted.com/reviews/virtus.html
Amazing this came from a random map maker.