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According to Find out if you need a visa, citizens of the Philippines usually need a visa to visit Canada, but are eligible for the Transit Without Visa (TWOV) program.
The Determine your eligibility β Transit without a visa details the requirements for people who may be able to transit through Canada without a visa. From what you have described so far, your niece is likely eligible for this program.
There are no specific documentation requirements for leaving the USA, other than that which the airline requires to allow you to board a plane. Check with her airline to ensure that she has the required documentation (at least a passport and a confirmed itinerary will likely be required).
If she is not eligible for the TWOV program, she will need to apply for a transit visa.