Depends. If the Earthworm Jim 1 for the PC is the Special Edition, then I'd go for the Steam Package. The Special Edition for the PC is THE best version, it has the best graphics, best sound quality, every level added in the Sega CD, and many other additions you may enjoy.
If it's the version packaged with Can O' Worms, than get the VC version instead, the COW version is one of the WORST versions.
If it's just emulated SNES or Genesis, than I'd say it's your pick on which you want.