Preheat your oven to 350°F and line 1-2 cupcake pans.
Start by combining the dry ingredients in a medium bowl, including the flour, baking soda, baking powder, and salt. Set this aside for now.
In a separate, larger, heat-proof bowl, combine the cocoa powder and dark chocolate chips. Now take your boiling water and pour it over the two chocolates ingredients. Whisk this mixture together until the cacao powder is dissolved and chocolate fully melted. Set this aside too to cool down.
Moving on to the next bowl, in a stand mixer fitted with the paddle attachment, combine the coconut oil, coconut sugar, and maple syrup. Mix on medium speed until combined, roughly 1 minute. If the maple syrup separates some from the oil, that's okay! There's water in maple syrup, which doesn't mix well with oil at this point.
Now add the eggs, one at a time, beating each one in until creamy.
Then add the greek yogurt and vanilla and once again beat your mixture until creamy.
Continue beating on medium-low speed and slowly pour in the cooled down chocolate mixture. Make sure that the mixture is no more than slightly warm when you add it. Beat until it is well combined.
Lastly, add your flour mixture to the batter, beating on medium-low speed until it is just incorporated. Make sure not to over-mix the batter, otherwise the cupcakes will turn out tough!
Divide the batter into the lined cupcake pan. You'll get between 12-16 cupcakes depending on how full you fill the liners. Some days call for smaller cupcakes and some days call for giant ones! Just make sure they're at least ⅔ full.
Bake at 350° for 20-25 minutes, depending no how full the liners are. Start keeping a close eye on them at the 18 minute mark. They'll be done when a toothpick comes out clean and the cake springs back when you press gently on it.
Remove from the oven and transfer to a rack to cool completely.