If I riposte a repeated Thwonk! do I counter both or only one stun?

If you use Riposte to counter a Thwonk! that has had its Repeat cost paid, you counter the entire spell, which includes both instances of the stun effect.

According to the rules of the game and the mechanics of Repeat:

1. Repeat is not a separate spell: When you pay the Repeat cost, you are not creating a second, separate spell on the chain. Instead, you are paying an additional cost to have the original spell execute its effect a second time. The entire package (the original spell plus the repeated effect) exists as a single object on the chain.
2. Countering the spell: Riposte targets "a spell." Because the repeated Thwonk! is a single spell object on the chain, countering it negates the entire execution of that spell.
3. No partial resolution: Since the spell is countered, it is removed from the chain and sent to the trash (Rule 412.1.a). Consequently, none of its effects—neither the first stun nor the repeated stun—will occur.

Summary: You counter the entire spell instance, meaning both stun actions are negated.