To prepare the marinade, in a food processor or blender combine the shallots, garlic cloves, basil, cilantro, olive oil, lemon juice, apple cider vinegar, salt, pepper, cumin and cayenne pepper. Puree until smooth.
Pat dry the chicken thighs with paper towels to remove any excess moisture and season the chicken with salt and black pepper.
Place the chicken in a large resealable bag or non-reactive container and pour the marinade over the chicken. Mix to combine making sure the chicken is coated evenly. Marinate at room temperature for 30 minutes or refrigerated up to 8 hours.
Preheat the oven to 375 degrees Fahrenheit.
Remove the chicken thighs from the marinade and place them skin side up on a rimmed baking sheet with or without a wire rack, or in a a baking dish.
Place in the oven and bake for 35 to 45 minutes or until the internal temperature reaches 165 degrees Fahrenheit. To crisp up the skin, broil the chicken for about 2 minutes making sure the chicken is about 6 inches from the heating source.
Remove chicken from the oven and allow it to rest, tented with aluminum foil for about 10 minutes. Serve.