Autosite reports that in April 2002, the CR-V outsold the RAV4 in the U.S., 12,341 to 6,764.
The CR-V has always outsold the RAV as long as I've been paying attention. My opinion is that its larger size makes it more appealing to the average shopper. Plus RAVs tends to be pricier sticker-wise, due to Toyota forcing you to take a lot of options when you only might want a couple.
I think you are correct, that currently the RAV can be had for much closer to invoice than the CR-V, which is still in great demand since its re-design.