In a large bowl, combine the water, sugar and yeast. Allow to sit for 5 minutes to bloom the dry yeast somewhat.
Add in the flours and salt and stir with a wooden spoon until the dough comes together. Add the chocolate chips and knead just a few times to smooth out the dough and distribute the chocolate, but do not over handle at this stage or it'll toughen the dough. Cover with plastic wrap and allow to rest and rise for 20 minutes.
Meanwhile, preheat the oven to 500°F. Line a baking sheet with parchment paper and set aside.
In a large bowl, whisk together the baking soda with 2 cups hot water. Set aside.
Transfer the dough to a very lightly floured work surface. Cut into six even pieces. Working with one at a time, roll each piece of dough into a long rope and shape into a pretzel, making sure to pinch the ends so that they don't unravel. Carefully dip the pretzel into the baking soda solution and then place on the prepared baking sheet. Continue until all the pretzels have been shaped, spacing them out evenly, allowing them some space to grow while baking.
Bake until golden brown and puffed up, 5 to 8 minutes. Carefully Remove the pan from the oven and allow to cool slightly.
Place the melted butter into a shallow dish. Then whisk together the granulated sugar and cinnamon in a separate shallow dish. Working with one pretzel at a time, while still slightly warm, carefully dip into the melted butter, turning over to coat both sides. Allow the excess butter to drip off before dipping into the cinnamon sugar and to fully coat. Place on a baking sheet and continue coating the rest of the pretzels. Serve immediately and enjoy!