Place a rack in the top third of an oven, then preheat. Line a standard muffin tin with paper liners, then coat with nonstick spray.
In a large mixing bowl, whisk together cornmeal, flour, black pepper, baking powder, baking soda, and Kosher salt.
In a separate mixing bowl, whisk together whole milk, sour cream, melted butter, sugar, and eggs until well combined.
Pour the dry ingredients into the bowl with the wet ingredients, along with chopped sage, chives, and the grated Gruyere. Use a spatula to fold the mixture until the dry ingredients are well incorporated.
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.
Allow the corn muffins to cool, then serve warm with butter or honey and a pinch of flaky sea salt.