personally i use aseprite for mspa-style art, which has yielded a lot of good results (i've attached some art i finished up yesterday for an example.) i've also heard clip studio paint is pretty decent, though i prefer aseprite since its built for pixel art and therefore everything is alised by default, which im not sure about in the case of csp.

https://www.homestuck.net/resources/booru/ also has a ton of handy guides to the art style overall, and theres a channel dedicated to it on the mspfa discord, so i'd reccomend checking those out too.