I have not personally used it myself, but I hear that Aseprite is really good for pixel art, Godot or otherwise. A quick Google search shows there are a few Godot plugins, but I couldn't find any for Godot 3+, just Godot 2.
I personally use Piskel for my occasional pixel art needs. It does not have any Godot plugins or anything, but the exports work fine as just sprite sheets. I also use Gimp for cleanup work and minor adjustments to pixel art and other images.
However, Aseprite, Piskel, and most other pixel editing software, should work just fine with Godot out of the box. As long as the software can export images as a sprite sheet, it should be fully supported without a problem. Those that can optimally pack sprites should work most of the time, though I have not personally tried this method in Godot, so you may want to do investigation on Godot's support of texture packing from the software of your choice.
