Staying in Bellagio on Lake Como at the end of the trip but flying out of Zurich Airport. What's the best option? Train back to Milan and then Milan to Zurich all in one day? Or should we consider changing our plans slightly and staying our last night in a different, but convenient town? (We are already staying 2 nights in Milan before going to Lake Como) Our flight out of Zurich is 5 p.m. on a Sunday, that might change suggestions.
I have taken the train in reverse direction... from Zurich to Milano...very nice trip...but I would not do it on the day that you are flying home for many reasons...too much traveling for one day 4 or more hours on a train then sit on a plane for 8 hours or so?
Then there is the risk of missing your 5pm flight...anything can happen to slow you down..even a two hour delay can put you in the airport too late to check in for an international flight....and a night in Zurich wouldn't be so bad...maybe cut the 2 nights in Milan at the start to just one...
Missing the flight is also a concern of mine. You are right, it would be a very long travel day - really two days by the time we reach home.
The itinerary to Zurich is now an hour faster as fast trains run the new Gotthard tunnel.
Personally, I would consider a ferry to Como, a taxi up to Como S.Giovanni station and boarding the train to Zurich there (sometimes the train stops in Como SG, sometimes you have to take a short ride to nearby Chiasso that is already within Switzerland). But by the time you get to Zurich airport, you have been traveling the best part of a day.
If you manage to break your trip in a point within Switzerland (for example, Lugano or Arth-Goldau) you have the guarantee that Swiss railways will do their best to run your train to the airport in exact timetable (if it gets delayed, they may run an extra train in front of it); however, Swiss railways are 99% reliable but not 100%.
If you do not want a long travel day and you want to be absolutely sure of getting to the airport in time, probably you should better break the journey at a point near the airport.
lachera gave you the best option. Personally I see no reason to go all the way back to Milan. From Bellagio Como is closer and you can intercept the same train coming from Milan at the Como SG station.
Having said that, I prefer to spend the last night in (or closer to) the city where I'm flying out of, in your case Zurich.
Actually in your shoes I would probably take the opportunity to spend my last night in Lucerne (Luzern), which in my opinion is nicer than Zurich and only 1 hour from the ZRH airport station by train.