Rinse the chicken thoroughly under cold running water. Pat dry with a paper towel. In an oven-proof baking dish combine the remaining ingredients. Add the chicken and turn several times to mix the ingredients.
Cover with aluminum foil and marinate for 2 to 4 hours in refrigerator.
Combine all the salsa ingredients in a bowl and mix thoroughly with a fork. Reserve.
Preheat oven to 375 degrees F.
Transfer covered baking dish to oven and bake for approximately 20 minutes, or until chicken is cooked throughout.
To serve, spoon a generous serving of salsa onto plate and top with 2 thighs.