ok i took some wip screenshots earlier so i can ACTUALLY ANSWER THIS

i used graphicsgale but you can definitely use photoshop with the pencil tool or sai with the binary tool or mspaint even (i know there are some tricks to using mspaint but idk them lol), anything that draws hard pixels

i start with w/e size canvas i need it to be (i wanted a 500x500 cover and i like smaller scaled pixel art so i used a 250x250 canvas) and sketch, then line on top of it, pretty basic. then i cleaned up some of the lines and picked some colors (i like using a limited palette so i aimed for 8 colors total but….. theres actually 10……….)

used the paint bucket on each area and started blocking out the shading, then changed the original black lines to other colors in my palette and doing pseudo anti-aliasing 

like that. thats pretty much it, then i keep messing with it until i like it!! i think i took it into photoshop in the end for some color adjustments but yeah