In a large bowl, whisk together the soy sauce, maple syrup, rice vinegar, minced garlic, grated ginger, sesame oil, black pepper, and red pepper flakes (if using). Add the chicken thighs and ensure they are fully coated in the marinade. Cover and refrigerate for at least 1 hour, or overnight for best flavor.
Preheat your oven to 400°F (200°C).
Line a baking dish with parchment paper or lightly grease it to prevent sticking.
Remove the chicken thighs from the marinade and place them skin-side up in the prepared baking dish. Reserve the marinade for later.
Bake in the preheated oven for 25-30 minutes, or until the chicken is cooked through and the skin is crispy. Baste the chicken with the reserved marinade halfway through cooking for extra flavor.
In the final 5 minutes of baking, switch the oven to broil. This will give the chicken skin an irresistible glaze. Keep a close watch to prevent burning.
Once cooked, remove the chicken from the oven and let it rest for about 5 minutes. Sprinkle with sesame seeds and chopped green onions before serving.