This is how I do it, not sure if it's the best solution but I can't find any other way else.
EDIT :
I didn't show the nodes because It works with most toon shader and not my specific one,
Though, this video is made with the assumption that you already have an Eevee toon shader and wanted to bake it, So I think I can see why It might be sort of confusing though, I apologize
I recommend you search for other videos about making toon shaders in Blender (or just download a shader). and then follow my video.
If it's the right shader You will be able to find a "Shader to RGB" node in the shader
and It will probably have "Diffuse BDSF" connected to it,
Because most Toon shader will always use that and it's the reason why you cannot bake it normally because you can only bake in Cycle and Cycle doesn't support "Shader to RGB"
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