Bike will be crossing the border without me

[Grumpy Goat]

Depends on what you call issues. As an immigrant to both countries the customs and immigration people can cause all sorts of issues, some being entirely baseless and time-wasting.

If I were you, I would ensure my niece has copy of your proof of ownership and current registration and insurance for the bike, as well as an open letter stating that she is simply transporting the bike through the US back into Canada.