Day 1: Morning, ~10am: Make the levain. Mixing all the ingredients for the levain together. Let rest 8-12 hours.
Day 1: Evening, ~10pm: Make the dough. Evenly combine levain, water, honey and salt together. Add bread flour and mix until a rough dough forms. Knead the dough until smooth ~10 minutes by hand. Cover and let rise overnight in a cool place (70-75F) for 8-10 hours.
Day 2: Morning, ~8am: Transfer the dough onto a lightly floured surface and divide into 8 even pieces (depending on how big you want your bagel bites to be). Work with one piece at a time, covering the rest to prevent them from drying out.
Shape the dough into a rough ball and flatten and shape into a disk. Make the edges thinner than the middle. Using a spoon, take a round scoop of cream cheese and drop it in the middle of the dough. Wrap the edges of the dough together and pinch to seal at the end. Now turn the ball seam side down onto a flour-free area of your work surface and cupping the ball in between palm of your hands and applying gentle pressure, turn the ball clockwise several times to seal the seams at the bottom. You should feel some tension being created between the dough and your work surface. If there isn't, wipe your work surface with a set towel and try again. Check the bottom to make sure it is well sealed, if it is not be patient and continue the clockwise rolling & sealing. Place the dough seam side down on a baking mat. Repeat with the rest. Cover and let rise 2-3 hrs.
Preheat the oven to 425F. Bring a pot of water and sugar to boil. Gently and gradually lower each dough ball into the water. If you lower them too quickly, they will touch the bottom and stick. If that happens, use a spatula and bring the dough free. Boil the dough for about 45 seconds, flip, and boil for another 30 seconds. You can boil a few at a time but make sure not to overcrowd the pot. Transfer the boiled bagels to a baking sheet lined with parchment paper or baking mat and repeat with the rest.
Make the bagel topping mix. Take the boiled bagels, brush will eggwash (optional), and dip the top into the mix. Alternatively, you can sprinkle on the topping mix. Place it back on the baking sheet and repeat with the rest. Transfer the tray of bagels to the oven and let bake for 25 minutes or until they are golden.