Welcome to the CruiseReviews forums, as well as to my favorite itinerary.
We've done the Canada/New England route several times, usually to/from Boston, as well as shorter cruises to Canada out of NY. One of our longer cruises was during the month of October. Weather can be pretty iffy then -- you can have warm sunny days or cool rainy days. There's no telling until a few days prior to the cruise. Most likely, you will experience several types of weather conditions, so my advice is to bring clothing that can be layered. A couple of sweatshirts and a windbreaker ought to do it, unless you are not accustomed to cool weather.
For motion sickness, I swear by green apples. This was told to me by a crew member when I was pregnant and could not take medications. Ginger also works for me, as does getting some fresh air.
What are your ports of call?