If my opponent attacks with yellow Vi and tries to stun my unit, I react with Janna to push it back to base. Does the Vi stun still apply?

No, the stun does not resolve.

Here's the sequence:

1. Vi attacks, and her "When I attack, [Stun] an enemy unit here" trigger goes on the chain.
2. You play Janna, Savior as a [Reaction]. Janna resolves first (LIFO) — she heals your units and moves Vi to its owner's base.
3. When Vi's trigger attempts to resolve, it needs to check "here" — Vi's current location — to define where the stun happens. Since Vi is now at base rather than the battlefield, the ability fails to find its source location and does nothing.

This is consistent with established rulings — the term "here" is referenced from the source of the ability, and that information is checked on execution (Rule 359.3.f.2). If Vi is no longer at the battlefield when her trigger tries to resolve, the instruction mistargets and the stun is not applied.