Try pptk (point processing toolkit). The package has a 3-d point cloud viewer that directly takes a 3-column numpy array as input, and is able to interactively visualize 10-100 million points. (It reduces the number of points that needs rendering in each frame by using an octree to cull points outside the view frustum and to approximate groups of far away points as single points)
To install,
>> pip install pptk
To visualize 100 randomly generated points in Python,
>> import pptk
>> import numpy as np
>> P = np.random.rand(100,3)
>> v = pptk.viewer(P)
screenshot of pptk viewer visualizing 100 random points
The documentation website also has a tutorial specifically on visualizing point clouds loaded from .ply files.