For marinade, simply combine all ingredients in a bowl and whisk well.
Place chicken thighs into a large (gallon) zip lock bag. Pour in the marinade. Try to get most of the air out of the bag before closing it. Lay the bag on it's side and make sure chicken and marinade are spread evenly. Place into a large pan to prevent leaks in the refrigerator and refrigerate overnight.
Preheat oven to 350 and lightly grease a 9x13 casserole dish.
Slice peppers and onion thinly and spread about 2/3 of the veggies in the bottom of the casserole dish.
Take chicken thighs out of the marinade and place them on top of veggies, side by side.
Spread the rest of the veggies around the chicken and pour marinade over the everything.
Bake for 70-85 minutes, depending of thickness of thicken. (Note: chicken breasts will take less time because there are no bones.)