Which ingredients can be used to create Navy Dye?
As Raven Dreamer said, Luminous Stone is one. However, Bladed Rhino Beetles also work, and can be found in many places, namely a tree directly right of the Plateau's opening cutscene.
Source: Dye - Zelda Wiki
The only item I've found that are Navy is "Luminous Stone", which you can mine from the ore deposits that glow at night.
Given the general frustrations with the Dye interface, I've not tried much more than that.