The Mininet is the most preferred one for SDN. As the topology configuration, connecting more controllers are feasible than NS3.

Both of them are really good for SDN environment and choices are to be made according to requirements, but for normal (and academic) scenarios, I would recommend Mininet, which offers a lot of flexibility and is able to model complex topologies. It is easier to install and configure Mininet in comparison to NS3.

Also, you can use Mininet-WiFi for wireless OpenFlow/SDN scenarios. It is a fork of Mininet which allows the using of both WiFi stations and access points.

If you use ns3, you can use the openflow switch for simulating the SDN, whereas in mininet, you can virtually configure the network and measure its parameters. Along with Mininet, you can use use Ryu Controller to control the bandwidth, delay etc in a virtual real environment. These things are not possible in NS3.

In my opinion, it depends on the traffic type that you have. If you have some real traffic traces or generator, I would definitely use Mininet, because it's the closest one to a final setup. However, if you don't have a clear way to generate traffic (similarly to an SDX environment), then ns-3 might be better.

Additionally, it also depends on your overall knowledge on these platforms, on whether this implementation is intended to be a long-term testbed, and on whether the idea to be implemented is too experimental (very ground-breaking/conceptual idea) or not.

By default, if you still hesitate, go for Mininet :)

As a continuation of my answer, I recommend your suggestion. Those who are new to SDN, better way of implementation is Mininet. Both Mininet and NS3 are simulators, only advantage of NS3 is huge dataset can be processed. But implementation part in NS3 is difficult than SDN.