Custom shader or texture2d? (Best way to color swap)

Texture2D makes it very easy. I don't know anything about Mip Mapping so lets assume I have unchecked generate Mip Maps in my texture import settings.

     // get all the pixels into an array of colors
     Color[] originalColors = myTexture.GetPixels();
     
     //find all the black ones and make them blue
     for (int i = 0; i < originalColors.Length; i++)
     {
          if (originalColors[i] == Color.black)
          {
               originalColors[i] = Color.blue;
          } 
     }
     
     //set the colors of the texture to the new colors
     myTexture.SetPixels(originalColors);
     
     //very important
     myTexture.Apply();

If you do have mip maps the functions mentioned above expect an integer index of the lowest map level I beleive. Something like that.