Can Vi Peacekeeper stun Ruin Runner?

No, Vi, Peacekeeper cannot stun Ruin Runner.

Vi's "When I attack" ability reads "[Stun] an enemy unit here" — which requires you to choose which enemy unit gets stunned. That makes it a targeted choice. Ruin Runner's protection ("I can't be chosen by enemy spells and abilities") prevents it from being a legal target for that choice. Even if Ruin Runner is the only enemy unit at the battlefield, Vi's ability will fail to find a legal target and do nothing.

This is the same interaction as Vi vs. Baron Nashor (FAQ #11345): any ability that requires you to choose a target is blocked by "can't be chosen" protection. It's distinct from programmatic selection effects like Vex, Apathetic, which automatically select the unit that triggered them without a choice — that bypasses the protection (FAQ #8772). Vi's ability requires an active choice, so it doesn't get through.