Lake Como/Milan situation

I would vote for staying in Milan the last night especially if you want to book time to see the Last Supper. We once arrived at Malpensa only to find out that there was a rail strike going on that involved certain trains. We had to get into Milan, change train stations, find the only trains running up to Como (none were running up the east side of the lake), take a local bus to Menaggio, then take the ferry across the lake to Varenna. That night Laura couldn't understand why none of her new guests hadn't shown up for dinner on the patio. We tried to describe the problems people were having getting to Varenna because of the strike. I'm a bit cautious and like to be within a taxi (or multiple transportation options) ride of my departure airport.

If you do end up staying in Milan and book tickets to the Last Supper, I can recommend the most wonderful non touristy restaurant nearby.

I think it is smarter to stay closer to the airport than Varenna. Keep in mind that the airport is about an hour from Milan so a taxi would be fairly expensive. There is train service from Centrale to the airport. I am not sure how you would make it to the airport from Varenna by 6, 6.30 am. Or are you trying to be at the airport at 9 for a noon departure?

In 2014, we had a one-night stay in Varenna on the night before our 11:50 a.m. flight back to the U.S. out of Milan's Malpensa airport and had no problem. There are a number of early a.m. train departures from Varenna. We picked the 6:23 a.m. departure. You're on the train for 75 minutes to Milano Central, with 5 stops. At Milano Central, you get off and change trains to the Malpensa Express. We arrived at the airport by 10 a.m. One thing to be aware of is that the Varenna train station is very small and isn't manned. We knew that but expected there to be a ticket machine, or a place in town where we could buy a ticket. Then we learned our situation might be complicated by the fact that there was a 24 hour train strike planned for the day before our need to take that early a.m. train. When we mentioned the situation to our tour leader (Varenna was a post-tour independent stay), she suggested we have our ticket in hand before arrival in Varenna. This was easy to do at a little travel agency in one of the towns on our tour. Had we traveled to Varenna by train from Milan, we'd have just gotten the return ticket while in Milan, but we were driven to Varenna by car.

Frank, the flight departs Milan at 11:20 am

Addendum to my earlier post, there is a 5:23 a.m. train departure from Varenna that gets to Milano Central at 6:40. That one being one hour prior to the one we took, I assume you'd arrive at Malpensa by 9 a.m.

Yes Vickie I would like to arrive by nine. Also remember, a lot of my concern is that we are traveling home on a Sunday. Living in Boston, I know that the commuter rail here really lessens their trains on the weekend.

Another vote for spending the night before your flight in Milan.
We stayed in a hotel near the Cadorna train station which is also closer to the historic center. Another plus is that the Malpensa Express train to MXP takes less time from Cadorna than from Milano Centrale.

Joe,

I'd also suggest staying in Milan the night prior to your flight, as that's a much "safer" method. Given the fact that you want to see The Last Supper, it seems like a logical choice. If you haven't been to Milan before, there are other sights you could see as well.

If you stay in one of the hotels near Milano Centrale, you'll have easy access to the Malpensa Express for the trip to the airport. You also won't have to wake up as early (Bonus!!!). You could also stay closer to Duomo and connect with the M.E. there (the trip is a bit shorter than from Milano Centrale). I'd suggest buying your ticket for the M.E. the day prior to travel, as that way there will be no delays on travel day when you're hauling luggage. DON'T forget to validate prior to boarding the train on the day of travel!

My husband and I were in the same situation and ended up spending the night before our departure at a place near the airport that we found on Airbnb. The host picked us up at the train station in Gallarate, and also drove us to Malpensa the next morning. Couldn't have been more convenient. I hated giving up the extra night in Varenna, but in the end I know we got a better night's sleep without worrying our train would be delayed, we'd oversleep, or whatever other issue may have caused us to miss our flight.

Much as I would hate to give up another day in Varenna, I would also stay in Milan for the last night for the peace of mind. If you don't have your train tickets in hand when you arrive in Varenna, there is a tobacco shop just past the mains square, Piazzza San Giorgio, that sells tickets, as well as a travel office near the docks. I'd check that on Thursday or Friday to have them.

Thank you all so much for the information and insight. It is truly appreciated