Preheat the oven to 325 degrees F (165 degrees C). Line a 12-cup muffin tin with paper liners.

Combine sugar and butter in a large bowl; beat with an electric mixer until light and fluffy. Add eggs, 1 at a time, beating briefly after each addition. Mix in chocolate syrup and vanilla extract. Add flour; mix until combined. Stir in chocolate chips. Scoop batter into the prepared muffin cups.

Bake in the preheated oven until tops spring back when lightly pressed, about 30 minutes; do not overbake. Cool in the tin for 5 minutes. Transfer to a wire rack to cool completely, about 30 minutes.

While cupcakes are cooling, combine chocolate chips, heavy cream, and instant coffee granules for the ganache in a microwave-safe bowl. Microwave at 30 second intervals, stirring between, until melted.

Dip the top of each cupcake in the ganache. Do not refrigerate.