Not an amazing source, but I am a history student and just completed history unit at Murdoch University (Perth, Australia) examining Australia and Asian relations and history.

The short answer is that yes, there is evidence of contact between the two. Matthew Flinders encountered Macassans during his voyage around Northern Australia (Great mistakes of Australian History, Crotty and Roberts (eds)), and there is further evidence that this had been in place for a reasonable amount of time, with boat building techniques and even some Macassan words being adopted by North Australian aboriginals. Also there are tamarind trees dated to the early 1700's (before colonisation).