Marking a rectangular region in a NumPy array as an image mask
It turns out that Numpy has various nifty ways of indexing. I found that my question can be solved by

clusterMask[clusterH - 2*S : clusterH + 2*S, clusterW - 2*S : clusterW + 2*S] = 1


As given in one of the comments, this link contains all information regarding numpy indexing:
https://docs.scipy.org/doc/numpy/reference/arrays.indexing.html