Prepare the pan. Place a rack in the top third of an oven, then preheat to 425°F/220°C. Line a standard 12-cup muffin tin with paper liners, then coat with nonstick spray.
Mix the dry ingredients. In a large mixing bowl, whisk together 1¾ cup (280g) cornmeal, 1 cup (120g) flour, ½ tsp black pepper, 1½ tsp baking powder, 1 tsp baking soda, and 1 tsp Kosher salt.
Mix the wet ingredients. In a separate mixing bowl, whisk together 1¼ cup whole milk (306g), 1 cup sour cream (or Greek yogurt; 240g), 8 Tbsp (113g) melted butter, 3 Tbsp sugar, and 2 large eggs until well combined.
Combine wet and dry ingredients. Pour the dry ingredients into the bowl with the wet ingredients, along with 2 Tbsp chopped sage, 1 Tbsp chives, and ⅔ of the grated Gruyere (reserve the rest). Use a spatula to fold the mixture until the dry ingredients are well incorporated.
Bake the corn muffins. Using a large cookie scoop, divide the batter evenly between the muffin tins. Sprinkle the remaining Gruyere on top of each corn muffin, then add a little cracked black pepper, if desired. Transfer to a preheated oven and bake for 14-17 minutes, rotating the pan halfway through cook time, until the tops have puffed up and are a light golden brown. Allow the corn muffins to cool for 5-10 minutes, then serve warm with butter or honey and a pinch of flaky sea salt.