This paper addresses integrating 6G Non-Terrestrial Networks (NTN) and Internet of Things (IoT) for joint user association (UA) and resource allocation in multi-tier heterogeneous networks (HetNets) powered by energy harvesting. The enhanced network model includes macro base stations (MBSs), small cell access points (SAPs), and additional 6G NTN and IoT components, all leveraging renewable energy. We introduce a two-timescale optimization framework to maximize long-term utility under energy neutrality constraints, crucial for 6G and IoT systems. The optimization dynamically adjusts UA and resource allocation each epoch based on variable energy states and distinct 6G NTN and IoT traffic patterns. To manage the complexity at scale, we propose low-complexity stochastic and robust algorithms tailored for this advanced setting. Simulations showcase significant gains over heuristic UA and greedy resource allocation, especially for 6G NTN and IoT. Our findings deliver key insights into efficiently handling energy harvesting dynamics and diverse traffic demands in sustainable future HetNets.