There's a great deal of argument about this -- traditionally it was identified as plague (Y. pestis) or smallpox, but the theory of typhus or typhoid has become rather prominent recently; the University of Maryland conference on historical diseases back in the 90's came to the conclusion that typhus, a lice-vectored fever, was the most likely culprit, while a DNA test by Papagrigorakis et al. in Athens on tooth pulp from victims is supposed to have strongly implicated typhoid, a disease with vaguely similar symptoms that is spread through tainted water. In the end, the roadblock we run into is that most of what we can do is argue about very limited literary evidence via historians whose medical credentials may be in some dispute; Papagrigorakis's DNA test is a fresh approach but problematic, and typhoid doesn't match as well with Thucydides's description, which is somewhat problematic.

What I advise you to discount as a temporary historical "fad" is the idea that the Plague of Athens was a viral hemorrhagic fever; this strikes me very much as a reaction to the widespread modern panic over the Ebola outbreak and relying on some very vague lines from the literary evidence (a bit not even included in Thucydides about "discharge," as well as Thucydides playing up the cruel romance of how caregivers were struck down by the disease when they exercised common human decency in nursing the sick and attempting to give proper rites to the dead).