Preheat the oven to 350F and spray a 12-cup muffin pan with baking spray.
Whisk together both flours, baking soda, baking powder, salt, and spices in a large bowl.
In a smaller bowl, whisk together the eggs and sugars until the eggs are smooth and lighter yellow. Add the pumpkin, oil, vanilla, and cider and whisk until smooth.
Pour the wet ingredients into the dry (and the cranberries if desired) and gently stir with a spatula to mix, being careful not to over-mix. If desired, let sit for 15 minutes to allow gluten to relax and starches to hydrate.
Spoon the mixture evenly into 12 muffin cups (about ¾ full) and bake for 25-30 minutes, until a toothpick comes out clean.