Preheat your oven to 400°F (200°C).

In a mixing bowl, whisk together the soy sauce, honey, apple cider vinegar, minced garlic, grated ginger, sesame oil, black pepper, and red pepper flakes until well combined.

Place the chicken thighs in a large zip-top bag or a shallow dish. Pour the marinade over the chicken, ensuring it is well coated. Seal the bag or cover the dish, and marinate in the refrigerator for at least 30 minutes, or up to overnight for more flavor.

Remove the chicken from the marinade (reserve the marinade for later) and place the thighs skin-side up in a baking dish.

Bake the chicken in the preheated oven for 25 minutes.

While the chicken is baking, pour the reserved marinade into a small saucepan. Bring it to a boil over medium heat, then reduce to a simmer for about 5 minutes to thicken slightly.

After 25 minutes, remove the chicken from the oven and brush it with the thickened marinade. Return the chicken to the oven and bake for an additional 15-20 minutes, or until the internal temperature reaches 165°F (74°C) and the skin is crispy.

Once done, remove the chicken from the oven and let it rest for a few minutes. Garnish with sesame seeds and sliced green onions before serving.