What is more natural vanilla beans or non gmo vanilla extract? Thank you.

To Lori T's point about "natural" being a sticky term.
Do you mean it as a descriptor (not altered since harvesting) or a term of praise? If the latter, what are you praising? For ex, expected health benefits?
But those aren't necessarily present in higher amounts in unmodified foods than in modified ones.
Keep in mind an old joke in the vegetarian movement - remember, arsenic is natural [and occurs in orange skins, though not in lethal doses].

Using the term "natural" gets you into sticky territory, because the flavor compounds which create the vanilla flavor are chemicals themselves. Those are natural. They are also chemically identical to other compounds created in a lab- which are derived from other "natural" and organic sources. So which is "natural" depends on your interpretation, really. Most vanilla beans are actually grown organically, but the farmers can't afford the certification fees- so they are not able to market them using the label. Personally, I'd rather use a real vanilla bean, or make my own extract- which is easy enough to do. That can be done using an organic vodka if you like- which would preclude the worry over GMO's. The majority of the vanilla farmers of Madagascar- where the majority of the world's vanilla is grown- are too poor to be able to afford pesticides, so that's not likely to be a problem. Either type you mention- the whole bean or the "Non-GMO" extract. Though I would think if you insist on using what is "natural"- the whole bean is the only thing that fits that bill. Vanilla extract does not exist in nature. It could be considered a sort of processed food in some ways- because the flavor must be extracted by some means.