I got this recently, but when I play it It recognizes my save data from the steam version. is there a way to make this use it's own saves for just the Gog version?

No probably because both steam and GOG version create the saves in the same folder. Only thing you can do is remove your steam save files and launch the game again.

Location for the save files is here:

%APPDATA%\StardewValley\Saves\