In a large bowl, combine honey, soy sauce, apple cider vinegar, minced garlic, grated ginger, 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 2 hours for more flavor.
Heat vegetable oil in a large skillet over medium-high heat. Remove chicken from the marinade (reserve the marinade) and add to the skillet. Cook for about 5-7 minutes on each side, or until the chicken is golden brown 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 until slightly thickened.
Add the pineapple chunks to the skillet with the chicken during the last 2 minutes of cooking, allowing them to warm through.
Drizzle the thickened marinade over the chicken and pineapple in the skillet, tossing gently to combine.
Serve hot, garnished with sliced green onions and sesame seeds.