Preheat the oven: Preheat your oven to 375°F (190°C). Lightly grease a 9x13-inch baking dish or a large oven-safe skillet.

Season the chicken: In a small bowl, mix together the salt, black pepper, cumin, and smoked paprika. Pat the chicken thighs dry with a paper towel, then rub the spice mixture evenly over both sides of the chicken.

Sear the chicken: Heat the olive oil in a large skillet over medium-high heat. Add the chicken thighs and sear for 3-4 minutes on each side, until golden brown. Remove the chicken from the skillet and set aside.

Sauté the aromatics: In the same skillet, add the diced onion and cook for 3-4 minutes, until softened. Add the minced garlic and chopped jalapeño, cooking for an additional 1 minute until fragrant.

Prepare the sauce: Stir in the diced tomatoes (with juices) and chicken broth. Bring the mixture to a simmer, then reduce the heat to medium-low. Return the chicken to the skillet, spooning the sauce over the top. Cover and let it simmer for 10 minutes.

Cook the rice: While the chicken simmers, rinse the rice under cold water until the water runs clear. In a medium saucepan, combine the rice, water, lime juice, and half of the chopped cilantro. Bring to a boil, then reduce the heat to low, cover, and let it simmer for 15-18 minutes, until the rice is tender and the liquid is absorbed. Fluff the rice with a fork and stir in the remaining cilantro.

Assemble the dish: Spread the cooked rice evenly in the prepared baking dish. Using a slotted spoon, transfer the chicken and sauce from the skillet over the rice, leaving any excess liquid behind. Arrange the chicken pieces evenly over the rice.

Prepare the queso: In a small saucepan, melt the butter over medium heat. Whisk in the cornstarch and cook for 1 minute. Gradually whisk in the milk, garlic powder, and onion powder. Bring the mixture to a simmer, stirring constantly, until it thickens slightly. Reduce the heat to low and stir in the shredded Monterey Jack and cheddar cheeses until melted and smooth.

Add the queso: Pour the queso evenly over the chicken and rice in the baking dish. Use a spoon to spread it out and let it seep into the layers slightly.

Bake: Transfer the baking dish to the preheated oven and bake for 15-20 minutes, until the queso is bubbly and the edges are lightly golden. For a crispier top, broil for 1-2 minutes at the end, watching closely to avoid burning.

Serve: Remove the dish from the oven and let it rest for 5 minutes. Garnish with additional chopped cilantro or sliced jalapeños if desired. Serve hot with warm tortillas, sour cream, or guacamole on the side.