The Embassy Suites is a good choice for a hotel in Niagara! Personally, my must-do's would obviously be walking down the path by the falls, and walking up Clifton Hill. There are a bunch of touristy attractions there like haunted houses and ripley's believe it or not , etc. I would say for most the Maid of the Mist is a must do - for me I am kind of afraid of it so I tend to pass. I also love doing the Skywheel in Niagara - it provides excellent views and is fairly inexpensive.
As for the city pass in Toronto, if you don't have a car, I dont think its worth it. If you will be downtown the whole time, then YES! I would say visit the Eaton Center for shopping, Younge & Dundas Square is right there as well and there's always stuff going on. I would say go to the CN tower if you haven't been before. I LOVE the ROM, and I think it's worth going to. I would skip the zoo and maybe do the science center, again depending on if you had a car. Casa Loma is pretty cool too but personally I find it kind of boring and not much to do. If you're into markets, Kensington and St Lawrence are the way to go! Ripley's Aquarium also opened recently and is awesome! The lines can get crazy but in my opinion it is a must do (and is right downtown). If time permits, try getting tickets to a Blue-Jays game! Sports in Toronto have such a good vibe and following!! Let me know if you have any other questions! Oh also the Subway is very easy to use and can make getting around a lot cheaper.