I use a function for doing that, and actually have put it in {R directory}\etc\Rprofile.site so that it will always be available for use.
cls <- function() {
require(rcom)
wsh <- comCreateObject("Wscript.Shell")
comInvoke(wsh, "SendKeys", "\014")
invisible(wsh)
}
cls()
To clear the console give
cls()
P.S. The function doesn't work the first time it's called and that's why I invoke the function immediately after declaring it in Rprofile.site. As I recall, you may be asked to install some program, in order for this to work.