Preheat oven to 375° F. Grease a large baking dish or roasting pan.
In a large bowl, whisk together molasses, Dijon mustard, apple cider vinegar, and apple cider. Add chicken and toss to coat. Let the chicken sit in the marinade for about 15 minutes.
Meanwhile, arrange onions, apples, garlic, and herbs in the bottom of the prepared dish. Season with salt and pepper; toss to combine. Place chicken on top; pour the remainder of the marinade over chicken. Season chicken liberally with salt and pepper.
Bake for about 55-60 minutes, basting the chicken at the 30-, 40-, and 50-minute marks. Baste once more after removing from the oven. The chicken is done when it reaches an internal temperature of 165° F. This can take as little as 35 minutes for small chicken breasts or as much as 70 minutes for very large chicken breasts. A meat thermometer is the best way to tell when your chicken is cooked through.
Garnish chicken with additional herbs, if desired.