There are a number of ways to define “deadliest.” How high is the fatality rate for those contracting a particular virus is one way. Ebola, Marburg virus, Lassa virus, and Lyssaviruses typically top this list–Lyssaviruses contains the rabies virus which has a nearly 100% fatality rate. The Ebola and Marburg viruses, according to Shannon Plaxton at Medscape, can have fatality rates of nearly 90%. Cases of these are relatively rare, however, compared to viruses that have caused highest death rates. In recent history Hepatitis (all kinds) is estimated to account for a million deaths annually, with HIV/AIDS still claiming almost 2 million victims each year. Influenza, by some estimates, still causes 250,000-500,000 deaths a year.
The third way of measuring the deadliness of a disease is by total victims claimed over time. By this measure the four most deadly viruses in human history are the bubonic plague, flu virus, smallpox, and HIV/AIDS. In the 14th century it’s believed that the bubonic plague, known as the Black Death, killed 75,000,000 people in half a decade. Smallpox, now eradicated, existed for thousands of years and throughout the 18th century claimed 400,00o lives a year in Europe alone. Smallpox killed hundreds of millions of people. The 1918 Spanish flu killed 50 million people by some recent estimates, though earlier estimates were lower. The World Health Organization estimates that 36 million people have died of HIV/AIDS since 1981. Compared to these killers, Ebola–while a certified, ruthless killer with a sky high fatality rate–has done little damage so far, killling just thousands.
correction: bubonic plague, as TheGCU helpfully points out in the comments, is not a virus but a bacterial infection. We apologize for the error.