Control alignment of two side-by-side plots in knitr
An alternative which worked for me: save the plots as files, then put the picture markdown on the same line (from here).
## Show images
 
You can save ggplot plot objects with ggsave.
Base plots are a bit more complicated, see for example here.
I'm putting this answer here because it helped me. Whether it's better for you or not depends on your situation.
To center two plots you can add fig.align='center'to your chunk options. If it produces one plot above the other add also fig.show='hold'. The result should be two centered graphs. 
So your final chunk option should look something like:
{r,echo=FALSE, out.width='.49\\linewidth', fig.width=3, fig.height=3,fig.show='hold',fig.align='center'}