In a large pot, heat oil. Season chicken on both sides with salt and pepper. Working in batches, brown chicken on both sides and transfer to a plate.
Add onion and saute for about 5 minutes. Then add garlic, cumin, and chilis; cook until garlic is soft and fragrant. Add tomatoes and 1 teaspoon salt and cook until tomatoes begin to break down. Stir in 1 cup water and return chicken and any accumulated juices to pot. Cover, reduce to a simmer, and cook for 25 minutes.
Remove several pieces of chicken and stir in rice, making sure it is completely submerged in liquid. Replace chicken, cover, and cook until rice is tender and liquid has been absorbed for 25 to 30 minutes more. Serve with lime wedges and cilantro if desired.