I own Witcher 3 GOTY edition on my Xbox One and I'm curious if I can transfer that ownership to GOG so I can play on my PC? Or if I should purchase the GOG version instead?

There was a galaxy promo a while back where you could get it for free if you had it in xbox. But that's over. Your need to purchase it at this point. If you're not anxious to play it soon, you can wait for a deeper discount. I suspect it'll be cheaper in December or January.