In a large bowl, whisk together soy sauce, pineapple juice, brown sugar, rice vinegar, sesame oil, garlic, ginger, black pepper, and red pepper flakes until the sugar is dissolved.
Add the chicken thighs to the marinade, ensuring they are well coated. Cover and refrigerate for at least 2 hours, or overnight for best flavor.
Preheat your grill to medium-high heat. Remove the chicken from the marinade, reserving the marinade for basting.
Grill the chicken thighs skin-side down for about 6-8 minutes, then flip and baste with the reserved marinade. Continue grilling for another 6-8 minutes, or until the internal temperature reaches 165°F.
Remove the chicken from the grill and let it rest for 5 minutes. Garnish with chopped green onions and sesame seeds before serving.