After migrating to Python from Matlab, it took me a while to get some 3D plotting methods I'm happy with in Python (with Jupyter notebook compatibility), but I think pyVista is the tool for the job. It handles everything on the back-end with VTK/ITK, provides a much-simplifed API, and seems to cover all the types of plots and filters I'm usually after (volumetric and/or isosurfaces from 3D gridded data), with interactive plots in Jupyter possible (via ITKwidgets). Very good documentation too, with lots of examples.
I haven't gone that deep yet, but it should also integrate nicely with Paraview I suspect (for more interactive data exploration and big data visualizations), and there's also - hopefully - a way to get interactive 3D plots in HTML output (TBC...).
For a bit more discussion on the topic, and some other alternatives, see Stack Exchange.
Here's a (rather crude) first attempt at plotting molecular orbital isosurfs with development code for ePSproc...
(Full code/API notes via Github/Read the docs.)