Make sponge: In a large bowl, stir together 1 tsp instant yeast, 4 cups bread flour, and 2 1/2 cups warm water until no dry spots remain. Cover with a dishtowel and let rise at room temperature until foamy and doubled in size, about 2 hours.
Make dough: Stir sponge until it collapses. Stir in ingredients for dough - 1/2 tsp instant yeast, 3 cups bread flour, 1 Tbsp honey, and salt. Once dough starts to come together, turn it out onto a lightly floured counter.
Knead dough, adding more bread flour as needed, until it forms a smooth ball, about 10 minutes total.
Form bagels: Roll the dough into an even ball and use a knife or dough cutter to divide it into 12 portions. Roll each portion into a ball, tucking the ends under so it is smooth on the surface. (See note below if making cinnamon-raisin bagels.)
Cover the balls of dough with a slightly damp paper towel and allow them to rest on the counter for 20 minutes.
Line two large sheet pans with parchment paper. Spray the parchment with nonstick cooking spray (don't forget this step or the bagels will stick).
Working with one portion of dough at a time, hold the dough with two hands and gently press your thumbs through the center to create a hole. Work your hands once around the dough to expand the hole. Place bagels on prepared sheet pans.
Rest bagels (15 minutes or overnight): Let bagels rest at room temperature for 15 minutes or refrigerate them, uncovered, overnight.
Boil and bake: Bring a large pot of water to a boil. Preheat oven to 450°F / 232°C.
When the water is boiling, stir in baking soda and 3 Tbsp honey. Gently drop the bagels into the boiling water, working in batches so that the bagels float on the surface with some space between them. Boil the bagels for 1 minutes on each side (2 minutes total). (Note: The easiest way to flip them is to push gently on one end of the bagel to submerge it - the bagel should flip right over. If some but not all of the batch of bagels includes cinnamon raisin bagels, boil those last to avoid flavoring the water.)
Return bagels to the prepared sheet pan.
If you’d like to add toppings, whisk together egg and 1 Tbsp water. Brush this egg wash over the top of the bagels and sprinkle on toppings.
Bake the bagels until golden brown, 12 to 14 minutes, rotating the pans halfway through baking.
Cool on a wire rack. Slice and serve!