I answered your PM about Ottawa and just saw this post.
We visit family in Montreal fairly often and our two main indoor winter activities are the Biodome and Exporail (train museum)
Biodome is sort of like an indoors zoo. There are 3 or 4 different ecosystems that you walk through (rain forest, laurentian forest I think and antarctic). Each area has different animals plants and trees and of course different temperatures.
Exporail is on the south shore of Montreal and is really only accesible if you are driving. It is an enormous building filled with restored trains and street cars from the really early days to modern times. Many of them you can climb into and pretend to drive, or see how the engines work. There is also a small room with an extensive model train system. For DS, his favorite part is that you can go outside and take a ride on a street car that then takes you to a short ride on a commuter train and then on a mini train. If you are visiting in the winter, I believe the outdoor train rides are not running. I forget what month they start up again, usually once the snow has melted.
There is also a tour you can do in Old Montreal where you basically walk underneath the city streets and see parts of the old city. I can't remember details, but we used to go there on school trips and it was fun. I will ask my mother - she teaches grade 3 & 4 in Montreal and takes her students on trips around the city.
DS - 10
DD - 8
Twin Girls - 6