Sift your almond and coconut flours through a fine-mesh sieve into a small to medium bowl.
Add the baking powder, baking soda, salt, cocoa powder, xanthan gum, and 1 cup of sweetener to the bowl with the flours. Stir together.
In the bowl of a mixer add your butter and beat. Beat in your eggs, one at a time.
Add vanilla, almond milk, sour cream to the bowl and mix together.
Add the bowl of dry ingredients to the mixing bowl and stir to combine. Add the instant coffee and vinegar and mix thoroughly.
Line the muffin tins with liners. Divide batter evenly among each of the muffin tins.
Clean the mixing bowl. Add the cream cheese to the mixing bowl and beat. Add the sweeteners, vanilla, and egg and mix again.
Add the chocolate chips and stir just until stirred in.
Add approximately 1 tablespoon of the cream cheese mixture to the cupcake mixture. Gently swirl the chocolate over some of the cream cheese mixture.
Bake at 350 degrees for about 20 minutes. You want them cooked through, but the cream cheese is slightly jiggly.
Store in the fridge.