Having researched this scenario myself (as a Canadian looking to possibly work remotely for a US company), I've found the following article helpful (although the tone may be a little too lighthearted IMO):
https://medium.com/inside-formstack/working-remotely-for-an-...
Unless the US company wants to set up a Canadian corporation / subsiduary, and issue you a T4 and withhold (and pay half of) your EI and CPP (or pay some an external company to do it for them), odds are you'll be working as a self-employed consultant / contractor and sending them invoices for your services. The one US company I've interviewed with so far said this is the way they handle paying foreign workers.
A word of caution, you'll want to make sure - for both your sake and your employer's - that the CRA doesn't view you as an employee if you're claiming to be a self-employed contractor (penalties would apply.) I'd recommend reading more about it here (with links to CRA's site in the article), and discussing this with your accountant before signing an offer:
http://www.taxtips.ca/personaltax/employees/employeevscontra...
I'd also suggest your offer be explicit in matters of control over work, ownership of tools, and other items that could make the CRA feel you're an employee versus a contractor.