Make the donut batter: Whisk together the flour, baking powder, baking soda and salt in a large bowl. Whisk together the eggs and sugar in a medium bowl until the sugar is dissolved, then whisk in the sour cream, milk and vanilla until combined. Make a well in the center of the dry ingredients and stir in the wet ingredients until just combined; the batter will be lumpy. Fold in the butter. Cover the bowl with plastic wrap and rest the batter for at least 15 minutes.
Make the cinnamon-sugar: Whisk together the sugar and cinnamon in a small bowl; set aside.
Make the vanilla glaze: Combine 2 tablespoons milk and the vanilla extract in a small bowl. Put the confectioners' sugar in a small bowl. Slowly whisk the milk mixture into the confectioners' sugar until smooth. If the mixture doesn't fall in a slow ribbon when you lift the whisk, drizzle in some of the remaining milk until it does.
Make the chocolate ganache: Put the chocolate in a heat-safe bowl. Bring the cream to a simmer. Pour the hot cream over the chocolate, shake the bowl to evenly cover the chocolate with hot cream and let the mixture sit for 1 minute before whisking until smooth. Set aside; keep warm.
Finish the waffle donuts: Heat the waffle iron according to the manufacturers' instructions. Lightly coat the waffle grid with nonstick pan spray and add 1/4 cup of batter to each waffle grid. Close the iron and cook until the waffles are lightly golden-brown, about 3 to 4 minutes. Transfer the waffles to a cutting board and repeat with the remaining batter.
Set a cooling rack over a rimmed baking sheet. Heat 3 inches of oil in a medium saucepan over medium-high heat until the oil reaches 350 degrees F on an instant-read thermometer. Use a 3-inch cookie cutter to stamp circles from the waffles; then use a smaller cookie cutter to stamp out a smaller circle from the center of each waffle. Add 3 or 4 waffles to the oil and fry until golden-brown and crisp, about 20 seconds on each side. Transfer the waffle donuts to the cooling rack and cool for just a few seconds before dipping both sides of each waffle donut in the cinnamon sugar. Repeat frying with the remaining waffles, dipping some of each of the following batch in the vanilla glaze and others in the chocolate ganache. Garnish the chocolate and vanilla-dipped waffle donuts with chopped nuts and/or sprinkles and serve warm.