Preheat the oven to 350°F (175°C) and line a baking sheet with parchment paper.
Fill a large deep pot (such as a stockpot) halfway with water and bring it to a boil. Once boiling, lower the heat slightly so the water stays at a gentle simmer rather than a strong rolling boil.
In a large bowl, combine the almond flour, tapioca flour, baking powder, and sea salt. Add ⅔ cup warm water, apple cider vinegar, and honey, then mix by hand until a smooth dough forms.
Divide the dough into 6–8 equal portions. Lightly wet your hands (or dust them with tapioca flour) and shape each portion into a ball. Flatten slightly and use your finger to make a hole in the center to form a bagel shape. Repeat with the remaining dough and place the bagels on the prepared baking sheet.
Carefully place 3–4 bagels at a time into the simmering water and cook for about 1 minute, or until they float. Remove them with a slotted spoon and return them to the baking sheet. Repeat until all the bagels have been boiled, then bake them for 10 minutes.
While the bagels are baking, mix all the Everything Spice Blend ingredients in a small bowl.
Remove the bagels from the oven, brush them with the beaten egg yolk, and sprinkle about 1 teaspoon of the spice blend over each bagel. Return them to the oven and bake for another 15 minutes, or until golden brown.
