The spring could be causing the creaking. When the spring compresses, the wire of the spring acrually goes into torsion. If you take into consideration the end coils which are in contact with the spring seat, they would have to rub againse the spring seat while going in torsion probably causing the creaking sound. Try wetting the spring and the seats with water and see it the creaking stops.
Cinelli Unica, BP Stealth, K2 Razorback, Steel Bianchi roadie, Bianchi Super GL, Specialized Stumpjumper, and 3 beach cruisers
Sounds are deceptive, humans aren't very good at locating their sources. Consider other possibilities, like the saddle. If you are pushing down on the saddle to test the rear shock, it could be tricking you.