Preheat oven to 350° F and line a baking sheet with parchment paper.
Fill a large pot halfway up with water and bring to a boil. Once the water has come to a boil, reduce heat slightly to keep water at a gentle boil.
Combine the almond flour, coconut flour, flaxseed, tapioca flour, baking powder and sea salt in a large bowl. Add ⅔ cup warm water, apple cider vinegar, and honey and mix (by hand) until a dough forms.
Use wet hands and form dough into 6 balls. Flatten the balls and use your finger to create a hole in the middle to create the bagel shape. Place the bagels on the prepared baking sheet.
Carefully drop 3 bagels in the boiling water until they float (about 30 seconds). Remove with slotted spoon and place them back on the baking sheet. Repeat until all bagels have been boiled. Bake the boiled bagels for 10 minutes.
Remove bagels from oven, brush with olive oil or aquafaba, and sprinkle each bagel with everything but the bagel seasoning. Return bagels to the oven and cook an additional 15 minutes.
Remove bagels once more, and carefully flip them over to make sure the bottom half cooks (should no longer be moist). Bake for an additional 5 minutes.
Cool on a baking rack for 10 minutes and then serve with your favorite toppings! Last 2 weeks in the fridge and a few months in the freezer.