Prepare the Marinade: In a mixing bowl, whisk together the soy sauce, brown sugar, pineapple juice, ketchup, apple cider vinegar, grated ginger, minced garlic, black pepper, and red pepper flakes (if using).
Marinate the Chicken: Place the chicken thighs in a large resealable bag or shallow dish and pour the marinade over them. Seal the bag or cover the dish, and let it marinate in the refrigerator for at least 2 hours or overnight for maximum flavor.
Preheat the Grill: Preheat your grill to medium-high heat.
Grill the Chicken: Remove the chicken from the marinade, reserving the marinade for basting. Grill the chicken thighs skin-side down for about 6-7 minutes until the skin is crispy. Flip the chicken and baste with the reserved marinade, grilling for another 6-7 minutes until the internal temperature reaches 165°F (75°C).
Grill the Pineapple: During the last 2-3 minutes of grilling, add pineapple slices to the grill, cooking them until caramelized and grill marks appear.
Serve: Remove the chicken and pineapple from the grill. Let the chicken rest for a few minutes before slicing. Serve the Huli Huli chicken with grilled pineapple slices on the side.