How to search for graduate schools that have Masters in Complexity Science/Complex Systems?
Try looking at speakers from conferences dealing with complex systems, e.g.:


European Conference on Complex Systems
NetSci


You can also search for other conferences (e.g. at http://www.conference-service.com) and then check the speakers. Furthermore, looking at affiliations from recent (say - last few years) papers you like my lead to some good trails.

When it comes to webpages being hubs from complex systems, try looking at:


http://www.complexssociety.eu
http://www.network-science.org


Some positions (including doctoral programs) and other resources are at http://www.barabasilab.com.

Also, some group websites are in my collections of links (Delicious: complexity and networks or search at my Pinboard).