When I try to boot the game it opens the fo4 boot menu, I press play it attempts to launch and then crashes. Is this because I turned off cloud sync or is it because I also had the game on steam? Any help would be appreciated.

No it doesn't need cloud sync.

Maybe try deleting/renaming the fallout4 folder seomewhere unter windows user's homedir / My Games with savegames and config last used.

If you played a lot with mods: there's one more "shared appdata" folder that'd be shared among gog/steam installs.