Season the chicken thighs with kosher salt on both sides and underneath the skins. Set aside briefly.
Make the rub. In a small bowl or measuring cup, combine the rub ingredients. Whisk until everything is well-incorporated.
Rub the chicken with the tomato rub on both sides, applying underneath the skins first.
Prepare a 9" X 13" baking dish. Brush the bottom of the dish with extra virgin olive oil. Arrange most of the sliced onions on the bottom. Arrange the chicken on top of the onions. Now add the rest of the onions and the sliced tomatoes between the chicken thighs. Pour in about ¼ cup of water from the sides of the baking dish.
Bake in the middle of your heated rack for 40 minutes or so, then, for crispy colored skin, put it under the broiler for a couple of minutes (watch carefully).
Leftovers & Storage: bring any leftover baked chicken thighs to room temperature then store in the fridge in a tight-lid container. If properly stored, they should keep well for 3 to 4 nights.
To make this with chicken breasts instead: use bone in, skin on breasts. Adjust the oven temperature to 375 degrees F and cook for about 30 minutes or until the chicken is cooked through and the juices run clear (internal temperature should be 165 degrees). Watch carefully because chicken breasts do tend to dry out, so make sure to get them out of the oven as soon as they are done.