Network-on-Chip (NoC) architectures and three-dimensional (3D) integrated circuits have been introduced as attractive options for overcoming the barriers in interconnect scaling while increasing the number of cores. Combining these two approaches is expected to yield better performance and higher scalability. This paper explores the possibility of combining these two techniques in a heterogeneity aware fashion. Specifically, on a heterogeneous 3D NoC architecture, we explore how different types of processors can be optimally placed to minimize data access costs. Moreover, we select the optimal set of links with optimal voltage levels. The experimental results indicate significant savings in energy consumption across a wide range of values of our major simulation parameters.