Monolithic 3D (M3D) technology enables high density integration, performance, and energy-efficiency by sequentially stacking tiers on top of each other. M3D-based network-on-chip (NoC) architectures can exploit these benefits by adopting tier partitioning for intra-router stages. However, conventional fabrication methods are infeasible for M3D-enabled designs due to temperature related issues. This has necessitated lower temperature and temperature-resilient techniques for M3D fabrication, leading to inferior performance of transistors in the top tier and interconnects in the bottom tier. The resulting inter-tier process variation leads to performance degradation of M3D-enabled NoCs. In this work, we demonstrate that without considering inter-tier process variation, an M3D-enabled NoC architecture overestimates the energy-delay-product (EDP) on average by 50.8% for a set of SPLASH-2 and PARSEC benchmarks. As a countermeasure, we adopt a process variation aware design approach. The proposed design and optimization method distribute the intra-router stages and inter-router links among the tiers to mitigate the adverse effects of process variation. Experimental results show that the NoC architecture under consideration improves the EDP by 27.4% on average across all benchmarks compared to the process-oblivious design.