In a large bowl, combine soy sauce, honey, rice vinegar, minced garlic, grated ginger, sesame oil, black pepper, and red pepper flakes (if using). Whisk until well blended.
Add the chicken thighs to the marinade, ensuring they are fully coated. Cover and refrigerate for at least 30 minutes, or up to 4 hours for more flavor.
Preheat your grill or a large skillet over medium-high heat. Remove the chicken from the marinade, reserving the marinade for later use.
Grill the chicken for about 6-7 minutes per side, or until fully cooked and the internal temperature reaches 165°F. If using a skillet, cook until browned and cooked through.
While the chicken is cooking, pour the reserved marinade into a small saucepan. Bring to a boil over medium heat, then reduce to a simmer for about 5 minutes to thicken slightly.
In the last few minutes of cooking, add the diced pineapple to the grill or skillet to caramelize slightly.
Once the chicken is cooked, remove it from the heat and let it rest for a few minutes. Slice the chicken and serve topped with the caramelized pineapple and drizzled with the thickened marinade. Garnish with sliced green onions and sesame seeds.