Put flour, sugar, and salt into large bowl and mix lightly. Add yeast and water, then knead together ingredients with hands. The dough will be sticky at first.
Once you have combined the ingredients into a manageable dough, take out the dough onto a flat kneading surface. Knead dough firmly with your hands until the dough is no longer lumpy and powdery, approximately 15min. Add sprinkles of water or flour as necessary to keep the dough manageable -- it will get elastic but pretty stiff.
Cut dough into 6 pieces. Shape each piece into a ball. Cover with plastic wrap or a damp paper towel to prevent drying.
Shape the dough. You can either poke a hole in the middle with your finger and stretch out into a bagel shape or roll out the dough into a rope and tie the ends together. The dough will expand, so leave a nice big hole in the middle.
Cover the bagels with plastic wrap and let rest for about 15 minutes (30-40 min during winter time).
In the meantime, fill a large pot with water and a teaspoon of sugar or honey and bring to a simmer. Preheat oven to 375 degrees.
When the dough is ready, carefully drop them into the water and let them simmer for about 15 seconds on each side, flipping them only once. The bagels should float. Keeping the water boiling too hard or flipping too much will cause the surface of the bagels to crinkle later. I usually boil two at a time.
Take the bagels out with a slotted spoon and blot excess water. If you would like to add toppings, do so now. For small or crumbly toppings such as sesame and poppyseed, dump out the toppings on a small plate and gently press the top of the bagel into the topping.
Put the bagels onto a baking sheet and let bake until brown, approximately 15 minute.
Note: You can use whole wheat flour and even ingredients such as cocoa, pureed spinach, pureed pumpkin/cinnamon/nutmeg to make different kinds (and different colors!) of bagel dough. Be sure to decrease the amount of added water accordingly -- I would try making the plain first to get an idea of what the dough should feel like.