Add black beans to a pot and cover with water by 2 inches.
Add halved onion, smashed garlic, bay leaf, olive oil, and optional spices.
Bring to a boil, then reduce heat and simmer uncovered for 60–90 minutes, or until tender. Add water as needed.
Salt during the last 15–20 minutes. Discard aromatics. Set aside 1 cup cooked beans.
Preheat oven to 425°F (220°C).
Place poblanos on a baking sheet and roast for 15–20 minutes, flipping halfway.
Cover with a towel to steam 10 minutes, then peel and de-seed carefully.
In a skillet, heat olive oil. Sauté onion and garlic over medium heat until soft.
Add venison and brown, breaking it up, for 6–8 minutes.
Stir in cumin, paprika, chili powder, tomato paste, black beans, salt, and pepper. Simmer 5 minutes.
Off heat, fold in cotija and chopped cilantro.
Fill each pepper with the venison-bean mixture.
Return to baking sheet and bake 10–12 minutes, until heated through.
Whisk yogurt, lime juice, garlic, cilantro, and salt in a small bowl.
Place stuffed poblanos on a platter.
Drizzle generously with cilantro crema. Garnish with extra cotija and cilantro.