In a mixer (or by hand), combine the sourdough starter, water, honey and salt. Add the flour a cup at a time until it pulls away from the side of the bowl. Knead for 5-10 minutes (this will take longer if hand kneading). Form the dough into a ball, cover and let rise somewhere warm until nearly double in size. For a long ferment, cover and refrigerate for 1-3 days. On baking day, let the dough come to room temperature for an hour or so out of the fridge before moving on.
Divide the dough into 6 or 7 equal pieces (roughly 3.5-4 ounces each). Roll each piece into a tight ball (use a dusting of flour, if needed). Poke a thumb through each dough ball and slightly stretch the opening to about 2 inches wide. Alternatively, the dough can be rolled into a snake. Pinch the two ends together to create the bagel shape.
Place each bagel on a parchment lined baking sheet. Cover the dough with a tea towel and let rise for 15-45 minutes. The dough will rise minimally during this time.
Preheat the oven to 425°. Bring a large pot of water to a boil and add 1 tablespoon of honey and 1 teaspoon of baking soda to the water. If adding toppings to the bagels, place toppings in a shallow dish.
Add 2-3 bagels to the boiling water. Let boil for 30 seconds (for a thin crust) to 2 minutes (for a thicker crust) on each side, flipping the bagels over halfway through. Using a slotted spoon, remove the bagels and place back on the baking sheet. When cooled slightly, but still wet, dip the top of the bagel in topping (or sprinkle over the top) and place back on the baking sheet. Finish boiling and dipping the rest of the bagels and place on baking sheet.
Bake the bagels for 20-25 minutes until golden brown. Let cool for 10 minutes. These are best on the day they are made. Store at room temperature.