Make the marinade: In a bowl whisk together 1/4 cup lime juice, 2 tablespoons honey, 1 tablespoon olive oil, 1 tablespoon white vinegar, 1 tablespoon soy sauce, 2 teaspoons liquid smoke, 2 teaspoons garlic powder (or 2 minced garlic cloves), 1–2 teaspoons chipotle chili powder, 1 teaspoon salt, 1 teaspoon ground cumin, 1 teaspoon smoked paprika, 1/4 teaspoon pepper, and 1/4–1/2 teaspoon cayenne (optional).
Prepare chicken and vegetables: Place pounded thin chicken breasts in a large freezer bag and add half the marinade; refrigerate. In another bag combine the reserved marinade whisked with 1/3 cup honey and add the sliced/quartered red onion, red and green bell peppers, and corn; refrigerate. Marinate chicken and vegetables separately 6–10 hours.
Cook the rice: Heat 2 tablespoons olive oil in a medium saucepan or large pan over medium heat. Sauté 1/2 cup chopped red onion 3–5 minutes until tender. Add 3 minced garlic cloves and 1 teaspoon ground cumin and cook 30 seconds. Stir in 1 1/2 cups long-grain rice and briefly toast.
Add the 14.5 oz drained black beans and 3 cups low-sodium chicken broth and bring to a boil. Reduce heat to low, cover, and simmer about 20 minutes until rice is tender, stirring once at ~15 minutes. Remove from heat, season with salt and pepper, then stir in 2 tablespoons lime juice and 1/2 cup chopped cilantro.
Make the chipotle-lime crema: In a bowl mix 1 cup sour cream, 2 tablespoons lime juice, 1/2 teaspoon salt, 1/4–1/2 teaspoon chipotle chili powder (start with 1/4 tsp), dash of cayenne if desired, and 1/4–1/2 cup finely chopped cilantro. Refrigerate until serving.
Stovetop chicken: Heat 2 tablespoons oil in a large skillet over medium-high until very hot. Remove chicken from bag and discard marinade. Add chicken and cook undisturbed 2–3 minutes until browned. Flip, cover, reduce heat to medium, and cook 5–8 more minutes until cooked through (internal temp 165°F). Remove to a cutting board and rest 3–5 minutes before slicing.
Stovetop vegetables: While chicken rests, add 1 tablespoon olive oil to the skillet, discard vegetable marinade, and add the peppers, onions, and corn. Cook, stirring occasionally, just until warmed through and lightly charred at the edges.
Grilling alternative—chicken: If grilling, let chicken come to room temperature 15–30 minutes, preheat grill to medium (375–450°F), discard marinade, and grill chicken 5–7 minutes per side until internal temp reaches 165°F. Rest 5 minutes before slicing.
Grilling alternative—vegetables: Discard vegetable marinade. Lightly oil peppers and onions and thread onions on soaked skewers. Grill onions ~10 minutes and bell peppers ~6 minutes, turning until tender and charred. Brush corn with oil, wrap in foil, and grill ~15 minutes, rotating; cool and cut kernels from the ear.
Assemble bowls: Divide cilantro-lime rice among bowls, sprinkle with shredded Monterey Jack cheese, top with fajita vegetables and sliced chicken, and finish with chipotle-lime crema.