NetSim supports all layers of the stack for IOT
Application - COAP
Transport - TCP / UDP
Routing - RPL, AODV (IPv6)
MAC/PHY - 802.15.4
NetSim supports simulation & emulation.
I would definitely recommend it over Cooja
Rather than provide you with list of differences, I'll give my view on the matter.
In my experience, running stuff developed in Cooja doesn't ever work in one go, except for really simple, really short stuff -- For any sizable project there are all kinds of problems that crop up and need to be resolved (and many cannot be). Also, if you learn Cooja there's a lot on the internals you need to learn that has no value later on in the industry.
NetSim has many libraries for various networking technologies (all layers of the stack) for which there is no equivalent in Cooja. (You have to pay for NetSim. But your school can get it at discounted price). NetSim has proven compliance with international standards, testing tools, validation tools, report generation, a much large community & user base, etc. etc. etc. There are also large code bases written in NetSim. There are professors, engineers, students, .. lots of people who know all the intricate details of NetSim.
So, my advice: If your school will pay for NetSim, buy NetSim and learn to use it properly. In the long run, it's a better decision. If you really can't get the money , then use Cooja.
NetSim is a professional tool with an easier to use GUI and a much faster learning curve. With just the GUI you can design the network, set parameters, enable various statistics, view plots and visualize via an animator. Then source codes in C can also be modified to write your own algorithms.
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