Difficult to guess...
You do sometimes gets clunks if a cargo container is slightly lose in it’s locks so that would be a candidate if you were sat towards the trailing edge of the wing, but if you were further forward, e.g, very close around Door 3 on a -300 you are not above the holds, you are sat above major components of the air conditioning system, the centre wing fuel tank with it’s associated pumps, valves,plumbing etc, and the main gear bays. I’m not sure what is meant by the hydraulics settling down...there’s certainly a lot of hydraulic system action during gear retraction but after that no so much and a lot of the system associated with the gear is actually depressurised once the gear is sat in it’s uplocks.