Finding the indices of the top three values via argmin() or min() in python/numpy without mutation of list?

Numpy includes an argsort function which will return all the indices. If I understand your requirement correctly, you should be able to do:

minidx = []
for cluster in sumErrors:
    minidx.append(np.argsort(cluster)[:3])

numpy.argpartition(cluster, 3) would be much more effective.