Can I thronk an attacking unit if it's going into an empty battlefield?

No, you cannot use Thwonk! on a unit moving into an empty battlefield.

According to the rules and FAQs regarding combat:

• Rule 429.1: A "Showdown" is opened when a move causes a battlefield to become contested while it has no units present from any player other than those that just moved. This is a non-combat showdown.
• FAQ: "When units move to an empty battlefield, are they considered 'attacking' or an 'attacker'? Ruling: No, units moving to an empty battlefield are not considered attackers. Attacker and defender designations only exist in combat."
• FAQ: "Moving to an unoccupied battlefield is not attacking and does not trigger attack-related effects."

Since Thwonk! specifically requires you to target an "attacking unit," and a unit moving to an empty battlefield is not considered an "attacker," the spell cannot be played on that unit. Combat only occurs when moving to an occupied battlefield.