Preheat the oven to 375 degrees F. Line a standard 12-cup muffin tin or jumbo 6-cup muffin tin with paper liners. Set aside.
In a bowl, whisk together the flour, ¼ cup of the cocoa powder, baking powder, baking soda, and salt; set aside.
In a separate bowl, whisk together the remaining ½ cup cocoa powder and the hot water until smooth.
In the bowl of a stand mixer fitted with a paddle attachment, beat the sugar, vegetable oil, eggs and yolk, and the vanilla on medium speed until combined, about 30 seconds. Add the cocoa powder mixture and beat until smooth. In three additions, add the flour mixture alternating with the sour cream until combined. Scrape down the sides of the bowl and add 2 cups chocolate chips. Beat until just combined, don’t over mix.
Divide the batter evenly among the prepared muffin tin cups, filling the paper liners all the way up. Sprinkle with the remaining ½ cup chocolate chips.
Bake in the center of the oven until the muffins have risen above the pan and a toothpick inserted into the center comes out clean, about 25-30 minutes for standard muffins, and 40 for jumbo.
Transfer to a wire rack to cool slightly before removing the muffins from the pan. Enjoy warm or at room temperature. Muffins can be stored in an airtight container at room temperature for 3 days.