Hi Luis!
There are some tools discussed in this thread: Convert color PNGs to 1 bit per pixel? - #3 by matt
Our team uses Aseprite on desktop for most drawing. @ryan.splendorr is our artist, and I know he has an iPad pixel art app that he likes drawing in, but I can't remember what it's called right now. Ryan, do you have anything to recommend?
Basically you can use any combination of things to wind up with black / white / transparent images. It'll probably be easiest to get nice results hand-drawing the pixels vs trying to convert them from images, but with tools like Ditherlicious, you could get cool results from other images. I know some folks have rendered 3D art in Blender, and used tools to wind up with dithered PNGs from that. So, whatever you're most comfortable with!