To my knowledge the cluster built by GCHQs is the currently the largest one. Does anyone know of a larger cluster currently being created? I found a 300 Pi cluster being built by this group http://megarpi.inf.unibz.it/index.php/about-us
We can't really tell since anyone (including me) might have already built a 5000-node cluster and simply did not publish their work.
The largest one that's made aware to the public is, in fact, the GCHQ cluster.
Update: This(link) is bigger.
I might have a 10,000 node Pi 3 cluster in my secret Pacific ocean underwater lair. Muhahahahahha!