Hi,
I'd suggest to have fist a technology requirement phase. The term "WSN" could mean a lot of things, and a lot of protocols. As a consequence, first check what protocols you want to use. As a second step, check if ns-3 modules support the protocols you want to use (and their variants). As an example, 802.15.4 is implemented in the lr-wpan module, but with some limitations. All this is explained in the manual and in the modules description.
This should be repeated for all the network parts, i.e., why/MAC, IP, routing, etc.
Most probably you'll find that some parts you need are missing. In this case you can develop them. Again, the right point to start is the tutorial and the manual.
Have fun,
T.