In this manuscript, a NDVI point cloud generator tool based on low-cost active RGB-D sensor is presented. Taking advantage of currently available ROS point cloud generation tools and RGB-D sensor technology (like Microsoft Kinect), that includes an inbuilt active IR camera and a RGB camera, 3D NDVI maps can be quickly and easily generated for vegetation monitoring purposes. When using low-cost sensors for vegetation index estimation, it is necessary to apply a rigorous methodology for extracting reliable information. In this paper, the methodology for NDVI generation using a low-cost sensor as well as experiments to evaluate its performance is presented. The experiments performed show that it is possible to obtain a reliable NDVI point cloud from a Kinect V2.