I second the answers that have already been given, but you might also consider updating the paper wherever it appears on the internet (your website, the arxiv). The referee(s) might not have started looking at your paper yet, and when they do, there's a decent chance that they'll download the paper from the arxiv or your website rather than looking at the copy that was actually sent to them by the journal.

(This comes from experience. I once had a paper where the referee ended up reading a version that wasn't quite final. I had caught some typos between putting the paper on the arxiv and sending to the journal; but the referee read the arxiv version, so the typos got caught again. This I think one can live with -- I wouldn't update an arxiv submission just to fix typos until the final version -- but if the changes were serious I think it would have been worthwhile.)