If you need to know the overall stiffness of your hydrogel (i.e. scaffold), then you can try by means of a texture analyzer.
In case you want to know how your cells "sense" each particular point of your substrate, then you can go with AFM and extract the Young’s Moduli from nanoindentation curves and Hertz model fitting, just as they told you before.
You can meaure the stiffness of your hydrogels by performing oscillatory rheological measurements of the elastic modulus G΄ and the viscous modulus G΄΄ as function of shear strain (Amplitude sweep experiment) and as function of frequency (Frequency sweep experiment). The amplitude sweep experiment will help you to determine the linear viscoelastic region (LVR) of deformation of hydrogels at increasing shear strains. Then you apply a strain value within the LVR to the frequency sweep experiment. You can also advise the following papers for your reference:
Cheng S., Clarke E.C.,Bilston L.E., Rheological properties of the tissues of the central nervous system: A review, Med. Eng. Phys., 2008, 30, 1318-1337.
Zuidema J., Rivet C., Gilbert R., Morrison F., A protocol for rheological characterization of hydrogels for tissue engineering strategies, J. Biomed. Mater. Res. B Appl. Biomater., 2014, 102, 1063-1073.
before measure any stiffness, my suggestion is draw a table for designing your experiments. use DX software. after that as last comments, you can use universal testing machine(UTM).