Understanding the receptivity of hypersonic flows to free-stream disturbances is crucial for predicting laminar to turbulent boundary layer transition. Input-output analysis as a receptivity tool considers which free-stream disturbances lead to the largest response from the boundary layer using the global linear dynamics. Two technical challenges are addressed. First, we extend recent work by Kamal et al. [1] and restrict the allowable forcing to physically realizable inputs via a free-stream boundary modification to the classic input-output formulation. Second, we develop a hierarchical input-output (H-IO) analysis which allows us to solve the three-dimensional problem at a fraction of the computational cost otherwise associated with directly inverting the fully three-dimensional resolvent operator. Next, we consider Mach 5.8 flows over a sharp cone and blunt cone with a 3.6 mm spherically blunt tip. H-IO correctly predicts that the sharp cone boundary layer is most receptive to slow acoustic waves at an optimal incidence angle of 10 • , validating the method. We then investigate the effect of free-stream disturbances on the blunt cone boundary layer, and identify two distinct vorticity-dominated receptivity mechanisms for the oblique first mode instability at 10 kHz and an entropy layer instability at 75 kHz. Our results reveal these receptivity processes to be highly three-dimensional in nature, involving both the nose-tip and excitation along narrow bands at certain azimuthal angles along the oblique shock downstream. We interpret these processes in terms of critical angles from linear shock/perturbation interaction theory.