Whisk warm water and yeast in the bowl of a stand mixer and let sit for 5 minutes.
Add the rest of the dough ingredients (minus flour and salt) and whisk until combined.
Add 2 cups flour and knead with the dough hook attachment for 2 minutes until incorporated.
Let sit for 15 minutes.
Add the rest of the flour and salt then knead for 5-10 minutes on low speed.
Transfer the dough to a greased bowl and let it rest for about 1-2 hours until doubled.
Prep a baking sheet with parchment paper, turn dough out onto a floured work surface and divide into about 8-10 pieces.
Shape bagels: Take each piece and shape it into a ball by gathering up the sides and pinching them together in the center. Turn the dough over so that the seam side is down on the work surface and gently form a smooth ball. This helps to develop the gluten structure.Then, using your thumb to poke a hole in the middle rotate your dough around your thumb as you smooth and shape the ring. The hole will need to be bigger than you think since it will shrink as the dough performs its second rise.
Place bagels on the parchment-lined baking sheet, evenly spaced, cover with a tea towel and let rise again while you prep the water bath.
Boil a large pot of water and preheat your oven to 425 degrees F.
Once your water has come to a boil add your baking soda and coconut sugar.
Place bagels into the boiling water (only about 3 at a time) and boil for 1-2 minutes on each side.
Remove the bagels from the water and place on a parchment-lined baking sheet and sprinkle toppings overtop.
Once all bagels have been boiled and topped, bake them for about 15-20 minutes until golden brown.
Remove from oven, let cool, and serve.