It depends, among other things on the size of your data stack, the output format , your budget and the purpose of the visualization.

• Gnuplot is great to take a quick look at data because it can read pure ascii and is easy to use. Is is also free. However, it is tough to generate plots that can be used for publishing and it does not run in parallel, so large data stacks are  problem. Personally, I use it a lot for line-graphs, but never for 2-D or 3-D.
• Matlab is nice if you have it, but requires more knowledge on behalf of the user (it is basically a programming language) and costs money. On the other hand, it deals well with 2-D and 3-D graphics and, as a commercial product, has a good support system.
• I'm not really familiar with SuperMongo, but it costs money and from what I can see is primarily for line-graphs and some 2-D work. Not for large 3-D visualization. I see no mention of volume rendering, or iso-surfaces.

As alternative, you can also look at VisIt and Paraview. Both are free, have a lot of functionality and can run in parallel, which is a big advantage when making 3-D plots. They also use a graphical interface based on GUI, which makes them (relatively) easy to use. Downside is that you are restricted in your data -format. (vtk is probably the best choice). Of course, IDL is still a good option, but has the downside that you basically have to learn a whole programming language.

To get back to your original question, I would never use gnuplot for 3-D plots. of the other two, Matlab is probably easiest, especially for beginners, because it has a good help function. From what I can see, I would not advice SuperMongo for 3-D, unless, maybe, for someone who is willing to spend a lot of time on it.

Thanks a lot for the answer, Allard.

I have a subscription of Matlab through my institute and am starting to use it. There was another plotting software named "Surfer" which is used in this context. But, is it usable for a beginner? I am using the platform Kbuntu 14.04. Can you give me the links to obtain Visit and Paraview?

I never used Surfer, but it costs money, so if you already have Matlab is seems a bit of a waste to by another piece of software. matlab is far more common, so it is a far more  useful skill to learn.,  Other  alternatives would be Tecplot, Vsc and Amira, but those (especially the last two) are enormously expensive.

I've included links for both VisIt and Paraview

As I said, the downside is the limitations on input format, though especially VisIt has a long list of possible formats. Both programs are still being developed and have support, on-line manuals and FAQs, but because people are basically doing it for free it may take a while before you get an answer if you send a request for help.

https://wci.llnl.gov/simulation/computer-codes/visit/

http://www.paraview.org/

Matlab has a strong GUI, so learning and making plots is quite easy as compared to GNU Plot.

However, I would suggest you to switch to Python. It has dedicated libraries for Astronomy and Astrophysics that goes by the name 'astropy' ( http://www.astropy.org/ ) . It has separate library for plotting 'matplotlib' (http://matplotlib.org/).

Python, being an open source high level language, has really good documentations and is very easy to learn. Following is a link to tutorial for making 3D plots:

http://matplotlib.org/examples/mplot3d/surface3d_radial_demo.html

You can find numerous other examples under the 'Gallary' section on matplotlib web page.

Look into ParaView and/or VisIT

If you go the python way then another excellent library for scientific 3D plotting and visualization is Mayavi from Enthought.

http://code.enthought.com/projects/mayavi/

It can be installed as part of Enthought's Canopy IDE, which is free for academic use.

http://code.enthought.com/projects/mayavi/