In a large bowl, mix together mashed bananas, creamy peanut butter, oil, granulated sugar, gluten-free flour blend, salt, baking soda, baking powder, apple cider vinegar and vanilla extract. Stir to combine.
Take one cup of the batter and place in a smaller bowl. Stir in the cocoa powder and water and mix to combine.
Spoon peanut butter mixture into muffin tin lined with cupcake liners. Add a rounded tablespoon of the chocolate batter to each muffin well and swirl with a toothpick or a knife. Top with chocolate chips.
Bake at 350F for 20-25 minutes, until muffin is lightly browned and a toothpick inserted into the center comes out clean.
Let cool in the pan for 5-10 minutes before serving.