If I Bone Skewer a Ruin Runner does it come in stunned?

Yes, Bone Skewer can stun a Ruin Runner even though the Ruin Runner has the ability "I can't be chosen by enemy spells and abilities."

According to the official RiftJudge FAQ #8682, a unit's "cannot be chosen" protection ability is only active while the unit is on the board. When the unit is in the opponent's hand, that protection ability is not active, which makes it a legal choice for Bone Skewer.

Sequence of events:

1. You play Bone Skewer. It resolves, and you choose a battlefield.
2. Your opponent reveals their hand, and you choose their Ruin Runner.
3. The opponent plays the Ruin Runner to the chosen battlefield (this is part of the resolution of Bone Skewer).
4. Because the text of Bone Skewer says "If they do, then do this: [Stun] it," the Ruin Runner is stunned as it enters the board.

Once the Ruin Runner is on the board, its protection ability activates, but it is already too late to prevent the stun from the resolution of the Bone Skewer effect.