At my Target, we only have a few Crystal Empire things out (we have the Wedding Castle and the FS Shining Armour / Cadance set, but that's it.) Our MLP merch is still under the "My Little Pony Canterlot" label next to the La-la-loopsy dolls.
The plushies were on-shelf at waist-level in a pink cardboard box.
If anybody remembers the wonky-faced Twilight Sparkle plush/pillow, she was kept in with the little girls' bedding, so if your Target doesn't keep the plushies with the main MLP merchandise, I would check there, too.