Proteins and polypeptides are characterized by low-frequency vibrations in the terahertz regime responsible for the so-called "boson peak". The shape and position of this peak are related to the mechanical properties of peptide chains. Amyloid fibrils are ordered macromolecular assemblies, spontaneously formed in nature, characterized by unique biological and nanomechanical properties. In this work, we investigate the effects of the amyloid state and its polymorphism on the boson peak. We used inelastic neutron scattering to probe low-frequency vibrations of the glucagon polypeptide in the native state and in two different amyloid morphologies in both dry and hydrated sample states. The data show that amyloid fibril formation and hydration state affect the softness of the polypeptide not only by changing the distribution of vibrational modes but also, and most significantly, the dissipative mechanisms of collective low-frequency vibrations provided by water-protein and protein-protein interactions. We show how the morphology of the fibril is able to tune these effects. Atomic fluctuations were also measured by elastic neutron scattering. The data confirm that any effect of protein aggregation on fluctuation amplitudes is essentially due to changes in surface exposure to hydration water. The results demonstrate the importance of protein-protein and protein-water interactions in the dynamics and mechanics of amyloid fibrils.