With the new bearings (and cups?) I would give it some time to wear in and seat the bearings. Then it'll need adjustment as there will be a little play in the cranks. If it still makes noise, it could be a crack in one of the cups. I usually hear a click when I stop pedaling on my old 1 speed, but it's from the rear hub.
New bearings + old cups...yes, it could also be from the hub even if it's new. Thanks Barry!