Preheat oven to 350F. Line 24 muffin cups with paper liners. Set aside.
In a medium bowl, beat together softened cream cheese, vanilla, egg, and sugar, until combined.
Stir in 3/4 cup of the mini chocolate chips and set aside.
To make the cupcake batter, whisk together the gluten-free flour blend, xanthan gum (if using), brown sugar, cocoa powder, espresso powder, baking soda and salt.
In a separate bowl, mix together hot coffee, vegetable oil, apple cider vinegar and vanilla extract.
Pour the wet ingredients into the dry ingredients and stir until combined.
Portion out the chocolate cupcake batter into each of the 24 muffin liners.
Dollop a tablespoon of the cheesecake batter on top of the chocolate cupcake batter.
Sprinkle remaining 1/4 cup of mini chocolate chips on top of each cupcake.
Bake at 350F for 25-27 minutes, until the tops are lightly browned and a toothpick inserted into the center of each cupcake comes out clean.
Let cool completely before serving.