In a large bowl, combine pineapple juice, soy sauce, brown sugar, ketchup, minced garlic, ground ginger, black pepper, and red pepper flakes (if using). Whisk until well blended.
Place the chicken thighs in the crockpot and pour the sauce mixture over the top.
Add the diced bell peppers and onion to the crockpot, stirring gently to combine.
Cover and cook on low for 6-8 hours or on high for 3-4 hours, until the chicken is cooked through and tender.
Once cooked, shred the chicken in the crockpot using two forks and stir it into the sauce.
Serve the chicken over cooked rice and garnish with chopped green onions.