We evaluate the performance and usability of mouse-based, touch-based, and tangible interaction for manipulating objects in a 3D virtual environment. This comparison is a step toward a better understanding of the limitations and benefits of these existing interaction techniques, with the ultimate goal of facilitating the integration of different 3D data exploration environments into a single interaction continuum. For this purpose we analyze participants' performance in 3D manipulation using a docking task. We measured completion times, docking precision, as well as subjective criteria such as fatigue, workload, and preference. Our results show that the three input modalities provide similar levels of precision but require different interaction times. We also discuss our qualitative observations as well as people's preferences and put our findings into context of the practical application domain of 3D data analysis environments.