Place the sliced onion and apple in the bottom of the slow cooker to form a base that keeps the chicken from sticking and adds flavor as it cooks.
Arrange the chicken thighs on top of the onion and apple slices in a single layer.
In a small bowl, stir together the apple cider, apple cider vinegar, honey, minced garlic, thyme, salt, and black pepper until the honey dissolves.
Pour the cider mixture evenly over the chicken.
Cover and cook on low for 6 hours or until the chicken reaches an internal temperature of 165 degrees F and feels tender when pierced with a fork.
Remove the chicken to a serving dish and cover it to keep warm.
Stir the cornstarch into 2 tablespoons of the cooking liquid until smooth, then add it back into the slow cooker.
Turn the slow cooker to high and cook for 10 to 15 minutes, stirring once, until the sauce thickens slightly.