Three dimensional integrated circuits (3D-ICs) are a promising solution to the performance bottleneck in planar integrated circuits. One of the salient features of 3D-ICs is their ability to integrate heterogeneous technologies such as emerging non-volatile memories (NVMs) in a single chip. However, thermal management in 3D-ICs is a significant challenge, owing to the high heat flux (~ 250 W/cm2). Several research groups have focused either on run-time or design-time mechanisms to reduce the heat flux and did not consider 3D-ICs with heterogeneous stacks. The goal of this work is to achieve a balanced thermal gradient in 3D-ICs, while reducing the peak temperatures. In this research, placement algorithms for design-time optimization and choice of appropriate cooling mechanisms for run-time modulation of temperature are proposed. Specifically, an architectural framework which introduce weight-based simulated annealing (WSA) algorithm for thermal-aware placement of through silicon vias (TSVs) with inter-tier liquid cooling is proposed for design-time. In addition, integrating a dedicated stack of emerging NVMs such as RRAM, PCRAM and STTRAM, a run-time simulation framework is developed to analyze the thermal and performance impact of these NVMs in 3D-MPSoCs with inter-tier liquid cooling. Experimental results of WSA algorithm implemented on MCNC91 and GSRC benchmarks demonstrate up to 11 K reduction in the average temperature across the 3D-IC chip. In addition, power density arrangement in WSA improved the uniformity by 5%. Furthermore, simulation results of PARSEC benchmarks with NVM L2 cache demonstrates a temperature reduction of 12.5 K (RRAM) compared to SRAM in 3D-ICs. Especially, RRAM has proved to be thermally efficient replacement for SRAM with 34% lower energy delay product (EDP) and 9.7 K average temperature reduction