To a blender, or food processor combine minced garlic, chopped onion, chipotles, coconut aminos, and apple butter. Pulse until well blended.
To a gallon sized bag, or large bowl, mix chicken thighs with marinade, salt and pepper. Fully coat chicken with marinade. Refrigerate for at least 3 hours, up to 6 hours.
Preheat oven to 425F. Line a baking dish with foil or parchment paper, spray it with cooking spray. Place marinated chicken thighs skin up in baking dish.
Bake for 30-45 minutes, until chicken is cooked, and no longer pink. Remove from oven, and allow to rest for 7-10 minutes, before serving.