The success of next-generation Internet of Things (IoT) applications could be boosted with state-of-the-art communication technologies, including the operation of millimeter-wave (mmWave) bands and the implementation of three-dimensional (3D) networks. With some access points (APs) mounted on unmanned aerial vehicles (UAVs), the probability of line-of-sight (LoS) connectivity to IoT nodes could be augmented to address the high path loss at mmWave bands. Nevertheless, system optimization is essential to maintaining reliable communication in 3D IoT networks, particularly in dense urban areas with elevated buildings. This research adopts the implementation of a geometry-based stochastic channel model. The model customizes the standard clustered delay line (CDL) channel profile based on the environmental geometry of the site to obtain realistic performance and optimize system design. Simulation validation is conducted based on the actual maps of highly dense urban areas to demonstrate that the proposed approach is comprehensive. The results reveal that the use of standard channel models in the analysis introduces errors in the channel quality indicator (CQI) that can exceed 50% due to the effect of the environmental geometry on the channel profile. The results also quantify accuracy improvements in the wireless channel and network performance in terms of the CQI and downlink (DL) throughput.