Preheat your oven to 350°F (175°C). Grease and flour the 9x13 inch baking pan.
In a large mixing bowl, combine the flour, granulated sugar, cocoa powder, baking powder, baking soda, and salt. Whisk together until well mixed.
Add the eggs, whole milk, vegetable oil, and vanilla extract to the dry ingredients. Beat with an electric mixer on medium speed for 2 minutes until smooth.
Carefully stir in the boiling water. The batter will be thin; this is normal.
Pour the batter into the prepared baking pan and bake for 30 to 35 minutes, or until a toothpick inserted into the center comes out clean.
Once baked, cool the cake in the pan for about 10 minutes, then use a toothpick or skewer to poke holes all over the cake.
In a separate bowl, mix the creamy peanut butter, powdered sugar, and milk until smooth. Carefully spread the mixture over the top of the warm cake, allowing it to fill the holes.
In a saucepan, heat the heavy cream over medium heat until just simmering. Remove from heat and add the chocolate chips. Stir until the chocolate is melted and smooth.
Pour the chocolate ganache over the cake, spreading it evenly.
Allow the cake to cool completely at room temperature, then refrigerate for at least 2 hours before serving.