3-Dimensional integrated circuits and systems are expected to be present in electronic products in the short term. We consider specifically 3-D multi-processor systems-onchip (MPSoCs), realized by stacking silicon CMOS chips and interconnecting them by means of through-silicon vias (TSVs). Because of the high power density of devices and interconnect in the 3D stack, thermal issues pose critical challenges, such as hot-spot avoidance and thermal gradient reduction. Thermal management is achieved by a combination of active control of on-chip switching rates as well as active interlayer cooling with pressurized fluids. In this paper, we propose a novel online thermal management policy for high-performance 3D systems with liquid cooling. Our proposed controller uses a hierarchical approach with a global controller regulating the active cooling and local controllers (on each layer) performing dynamic voltage and frequency scaling (DVFS) and interacting with the global controller. Then, the online control is achieved by policies that are computed off-line by solving an optimization problem that considers the thermal profile of 3D-MPSoCs, its evolution over time and current time-varying workload requirements. The proposed hierarchical scheme is scalable to complex (and heterogeneous) 3D chip stacks. We perform experiments on a 3D-MPSoC case study with different interlayer cooling structures, using benchmarks ranging from web-accessing to playing multimedia. Results show significant advantages in terms of energy savings that reaches values up to 50% versus state-of-the-art thermal control techniques for liquid cooling, and thermal balance with differences of less than 10oC per layer.