A problem of the mathematical modeling and analysis of noise-induced transformations of complex oscillatory regimes in hierarchical population systems is considered. As a key example, we use a three-dimensional food chain dynamical model of the interacting prey, predator, and top predator. We perform a comparative study of the impacts of random fluctuations on three key biological parameters of prey growth, predator mortality, and the top predator growth. A detailed investigation of the stochastic excitement, noise-induced transition from order to chaos, and various scenarios of extinction is carried out. Constructive abilities of the semi-analytical method of confidence domains in the analysis of the noise-induced extinction are demonstrated.