I think that all you need is a health certificate that was issued within 10 days of when you enter the country and proof of rabies vaccination; there's no quaratine period. I don't know of any pet friendly hotels, but I'll see if I can find any.
Have a great trip!
ETA: I found this site:
http://petfriendly.ca/list/ontario.php Quote:
Niagara Falls:
Best Western Fallsview
Camelot Inn Niagara Falls
Econo Lodge West of the Falls
Niagara-on-the-Lake:
A Connoisseur's Cottage
Country Side B&B
For-Rest Villa B&B
Harbour House Hotel
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