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You can write a C++ or python ROS node that constructs and publishes an rviz marker: http://wiki.ros.org/rviz/DisplayTypes/Marker . POINTS or TRIANGLE_LIST marker types would probably work.

If you want something more like matlab, but don't want to use matlab for some reason, you could try using the 3d plotting in the matplotlib python package: http://matplotlib.org/1.3.1/mpl_toolkits/mplot3d/tutorial.html