It depends on what you want to optimize.

You have an interesting comparison of several approaches in this chapter:

http://dgavalas.ct.aegean.gr/en/iframe_files/papers/2009/Clustering-chapter.pdf

Sincerely

QualNet   — A graphical scenario design and visualization tool. In Design mode, you can set up terrain, network connections, subnets, mobility patterns of wireless users, and other functional parameters of network nodes.   In Visualize mode, you can perform in-depth visualization and analysis of a network scenario designed in Design mode

Castalia is a Wireless Sensor Network simulator for early-phase algorithm/protocol testing built at the Networks and Pervasive Computing program of National ICT Australia. It supports realistic channel and radio models, a key element for accurate early-phase WSN simulation

I think ns3 is a good choice cuz it has a GUI and somehow its interface  can be considered as user friendly 

good luck

NS3, OMNet++ and GNS3 are tools for these cases and can be used to give you best result.

NS-2, NS-3 are the most common used simulators

I think the best simulator for clustering WSN algorithm is the network simulator called NS-2 2.34 that is used for  designing the network scenario which executes the  PSO  ( Particle Swarm Optimization) algorithm to form clusters and selecting cluster heads in order to reduce the energy consumption  of sensor nodes.

NS3, OMNet++ and GNS3 are tools for these cases and can be used to give you best result.

And even for clustering WSN algorithm is the network simulator called NS-2 2.34 that is used for  designing the network scenario which executes the  PSO  ( Particle Swarm Optimization)

I think for clustering OMNET++ and Castalia is best. I have work on it. It is really easy to write a code.

I would definitely say NetSim. It comes with build in algo's as well as an easy interface to MATLAB. So you can run any clustering algorithm you want in MATLAB and then do the network simulation part in NetSim. The interface is in "run-time" which means you can dynamically alter the clustering during the simulation if you wish.

http://www.tetcos.com

I would recommend NetSim (https://www.tetcos.com). We ended up wasting a lot of time trying to get things to work on NS3 / OMNET.