In the present study, a multi-variable comparative study of the effect of microchannel heat sink configurations on their thermal performance is conducted by numerically simulating three-dimensional fluid flow and heat transfer in multiple microchannel heat sink configurations. Thermal analysis is performed to investigate a novel wavy-tapered channel configuration of microchannel heat sinks with directionally alternating coolant flow for high-end electronics cooling. Simulations were conducted at different tapering and aspect ratios, focusing on how effectively previously proven geometric enhancements combine with one another in novel ways. Results confirmed the superiority of wavy channels over straight channels due to the development of the secondary flow (Dean Vortices), which enhance the advection mixing and consequently the overall heat sink thermal performance. Moreover, width-tapering of the wavy channel showed improved channel performance in terms of thermal resistance compared to untapered wavy channels. Almost 10% improvement in thermal resistance is obtained with width tapering. Also, the thermal performance showed a strong dependency on channel aspect ratio. Overall performance suggests that optimum tapering and aspect ratio conditions exist. The numerical investigations are then extended to novel heat sink design includes wavy tapered microchannels with directionally alternating flow to improve heat sink thermal performance. A 15% reduction in thermal resistance and highly improved substrate surface temperature distribution uniformity are obtained using alternating flow compared to corresponding parallel flow channels.