There are currently only small differences. Using the chunk inset takes a bit more time, unless you set up shortcuts, because you have to insert the inset, then insert the options. The main advantages are simply that it is marked as a chunk, and you do not have to manually enter "<<>>=" and "@". Sometimes I forget whether it is "<>=" and sometimes I forget the equals sign so this is nice for my bad memory. If you want to get fancy, you can customize the font size and color within the chunk inset (you could do this for ERT also but that would apply for all ERTs, not just knitr chunks). If interested, see Help > Customization in LyX.
We hope to implement some features that might enhance the use of chunk insets over ERT. For example, it would be nice to navigate chunk insets in the outline pane. This is http://www.lyx.org/trac/ticket/7790
It would also be nice to ensure that knitr chunks start and end with newlines. This would prevent some not-so-rare problems. This is http://www.lyx.org/trac/ticket/8875
It comes down to a matter of preference. I prefer the chunk inset, but note that the author of knitr prefers ERT.