Preheat the oven to 350°. Line 20 muffin-pan cups with foil liners.
In a bowl, using an electric mixer, beat the cream cheese with the sugar, egg and salt until smooth. Stir in the chocolate chips.
In a large bowl, whisk the flour with the sugar, cocoa, baking soda and a pinch of salt. In a small bowl, whisk the water with the egg, vegetable oil, vanilla and vinegar. At low speed, beat the liquid ingredients into the dry ingredients until a smooth batter forms.
Spoon the batter into the prepared muffin cups to fill them halfway. Spoon a heaping tablespoon of the cream cheese filling into the center of each cupcake, then sprinkle the almonds and sugar on top.
Bake the cupcakes in the upper and lower thirds of the oven for 25 to 30 minutes, or until puffed and springy to the touch. Switch the pans halfway through baking. Unmold the cupcakes; let cool on racks before serving.
The baked cupcakes can be frozen for up to 5 days.