Are you arriving at your hotel in Zurich late afternoon? Or the airport? Are you staying both nights in Zurich or one night in Zurich, one in Lucerne? Is this your first trip to Switzerland?
Most people will probably recommend to focus on Lucerne. While I think it is very beautiful there, I also love shopping/dining in Zurich and if you have a Swiss Pass of some kind, you can take trains, buses, trams to your heart's content in a very stress free situation .
I am actually planning to spend a couple hours shopping in this area of Zurich because it has the most amazing toy store I have ever been in (if you appreciate craftsmanship of wooden toys):
http://www.afar.com/highlights/a-wondrous-toy-shop-in-the-altstadt
I am the type that likes to cram a lot into a short amount of time and as long as you plan well, I think you can spend a few hours shopping/eating in Zurich, seeing Mt Pilatus (minus the boat ride) and shopping/seeing some of Lucerne before heading to Chur. On my last trip...I did something very similar. I spent some hours shopping/dining in Zurich. Stayed in Zurich. Went to Lucerne the next day and on to Zermatt that same day! I got it all in and loved it.
When I was in Switzerland, trains and transport were so reliable and easy that it was almost scary (in a good way). The SBB site is awesome. And, yes, you can allow for tight connections and make them just fine. I also heard good things about using luggage lockers in the train stations.
SBB SITE:
http://www.sbb.ch/en/home.html
As for the boat, I have motion sickness concerns also which is why I did not do the boat. I have had several students I teach tell me they were OK on the boat but because they were also jet lagged when taking it, they said it was not "ideal." You can see Pilatus very easily without the boat aspect. I believe they call it the Silver Round Trip versus the Gold.
And that is WONDERFUL that you are doing the Bernina! The train ride IS the attraction. You will be in awe and yes, you will get plenty of alpine views.
