When I play Thwonk and repeat it, can my opponent still negate the effect with either Not So Fast?

Yes, your opponent can use Not So Fast to counter your Thwonk! spell.

Ruling

According to FAQ #62 and the card text for Not So Fast, it can counter an enemy spell or ability if that spell or ability chooses a unit or gear that the opponent considers "friendly."

• Thwonk! reads: "Stun an attacking unit."
• Because Thwonk! targets a unit, it qualifies as a spell that "chooses a unit."
• When you play Thwonk! to target an attacking unit controlled by your opponent, that unit is "friendly" to them. Therefore, your opponent may use Not So Fast to counter the spell.

Regarding Repeat

Regarding your use of Repeat on Thwonk!:

1. Repeat is an optional additional cost paid during the "Pay Costs" step of playing the spell (Rule 746.1).
2. When you pay the Repeat cost, the spell is placed on the chain as a single item that will execute its effect twice (FAQ #8135).
3. Because the spell is played once, your opponent only has one opportunity to respond to the entire chain item.
4. If your opponent plays Not So Fast to counter Thwonk!, the entire spell is countered, including both the initial effect and the repeated effect (Rule 412.1.a).

Summary

• Can they counter it? Yes. Because Thwonk! targets a unit your opponent controls, they consider that unit "friendly" and may use Not So Fast to counter the spell.

Note: I could not fully verify this ruling against the retrieved rules.