Got it! Thanks!
I agree that it is more convenient to take the train from Malpensa to Milano Centrale, and then local train to Varenna. Though, the boat trip from Como to Varenna via Bellagio is very scenic, and you can also stop in Menaggio or Bellagio before you arrive at Varenna. Also the car trip is nice and could allow you to see some villages worth a visit. Local trains from Milan to Varenna are the fastest way to arrive, but do not expect very high comfort on local trains. So it is up to you
#do not expect very high comfort on local trains.#
I found the Trenord trains on this route much better in 2016 than when I first used it in 2013.
We are also planning a trip like this, but in August. Is it possible to buy these boat tickets in advance? I’m having trouble finding a website where I can do this. Thank you!
No, they do not sell online.