I am a US citizen and my wife is Chilean. We live in Chile and we will be traveling to USA in June. Chile is part of the VWP. Our trip is for 45 days. during that time we will be traveling to vancouver for 5 days. Will there be any problem for my wife to re-enter the United States after being in Canada for 5 days? She will still be within the 90 day period.
Your plans will be fine. As long as there are less than 90 days between your first arrival in the US, and last departure from the US, then there will be no problem. The VWP 90-day clock keeps ticking for the days you are in Canada, but that's not an issue for you.