Add the orange zest & juice, lime zest & juice, garlic, jalapeno, olive oil, cumin, oregano & kosher salt to a large bowl. Whisk to combine. Add in the chicken thighs & yellow onion. Toss to combine. Set aside to marinate for at least 20 minutes or marinate in the refrigerator (covered) for up to 8 hours.
Preheat oven to 425 degrees F, arranging the oven racks such that one is in the center of the oven & one is 4-6 inches under the broiler. Line a large rimmed baking sheet with foil for easy clean up, as desired, and set aside.
Transfer the marinated chicken & onions to the prepared baking sheet, draining & discarding any excess marinade. Bake on the center rack for 15-18 minutes, depending on the thickness of your chicken thighs. The chicken should be nearly cooked through. Remove the chicken from the oven to shred, and meanwhile preheat the broiler.
Carefully shred the chicken into bite-sized pieces - you can do so using 2 forks, or my favorite trick: pop the chicken thighs directly into in a stand mixer & let the paddle attachment do the work for you (I swear this works!). Transfer the shredded chicken back onto the baking sheet.
Place the baking sheet under the broiler. Broil 4-5 minutes, turning the pan halfway through, until the chicken carnitas are browned & slightly crisp.
Serve the carnitas in tortillas for tacos or a bowl with rice & beans for burrito bowls, finishing with your favorite taco night toppings of choice.