Preheat oven to 350 degrees. Line muffin tin with 12 paper baking cups and set aside.
In a large bowl whisk together the flour, salt, cocoa powder, baking soda, baking powder, and salt.
Beat together the sugar and eggs. Add the milk, butter, sour cream, and almond extract, mix well.
Add the dry ingredients to the wet ingredients and stir just until combined. Fold in the chocolate chips. Spoon the batter evenly into the prepared muffin tin.
In a medium bowl beat together the cream cheese, sugar, egg yolk, and vanilla until well combined. Spoon about 1 Tablespoon of the cheesecake mixture onto the top of each muffin. Swirl the cheesecake mixture throughout each muffin using a toothpick.
Bake muffins in the preheated oven for 18-23 minutes, until a toothpick inserted in the center comes out clean.