Freehand-based interaction techniques (FITs) are an emerging technology of importance for effective virtual reality (VR). In this regard, most modern head-mounted displays, such as the Oculus Quest, are equipped with inside-out cameras for egocentric hand tracking and natural hand gestures recognition. Following this technological evolution, we have developed an agent-based modeling and simulation VR application, called BoidVR, focused on freehand-based interaction with simulated agents. Our system enables users to view and interact with both the agents and virtual environment using FIT-based tools. We illustrate a number of specific gestures that allow users to manipulate the virtual environment and affect agent behaviors. Finally, we conduct a user experiment in which we evaluate the usability and user sentiment of our BoidVR application.