\documentclass{article}
\begin{document}
<<setup, include=FALSE>>=
library(knitr)
knit_hooks$set(crop = hook_pdfcrop)
@

Cropped.
<<test-a, crop=TRUE, fig.width=3, fig.height=3, cache=TRUE>>=
plot(1)
@

Not cropped.
<<test-b, fig.width=3, fig.height=3>>=
plot(1)
@
\end{document}
