Difficult question. I know that Matlab has some very strong Machine Learning libraries which make it extremely convenient to experiment. As much as I like GNU R and FOSS in this case I would say Matlab has the upper hand.

For one it has a huge userbase which posts code examples and solutions to various problems. Another being that Matlab has nice Machine Learning libraies in my opinion.

There are e.g. some interesting video lectures from stanford about this topic by Andrew Ng http://www.stanford.edu/class/cs229/ && http://www.youtube.com/view_play_list?p=A89DCFA6ADACE599 )

In the first lecture the question comes up and he has the same opinion.

I think eventually GNU R will be better but that will still take some time.