Just came back this week from a trip that had us train through Switzerland and into Northern Italy on our way down to CT. Didn't stop in Switzerland this time around, but have spent lots of time there in the past. What you're planning sounds like a great combo of mountains and Mediterranean!
I would look at flying into Zurich (or Bern or Basel) with the idea of making the Bernese Oberland your home base. That area has lots of the Swiss charm you think of when you picture Switzerland, and is very easy to get to, get around in and then connect to your next destination. Interlaken is the natural hub, but if I had my choice, I'd choose one of the towns in the nearby Lauterbrunen Valley (Gimmlewald, Murren or Wengen) as my base and enjoy as much time as I could exploring that area.
When you're ready to go to Italy, it's easy to connect to the train that runs through nearby in Spieze that will take you through (and under) the Alps all the way to Milan. No matter where you're coming from in Switzerland, Milan is the natural point to make the connection to the train that goes directly to Cinque Terre. A good half-way point between that area of Switzerland and CT would be Milan, but you might also want to look at stopping for a night or two in Stresa, which is a lake town in northern Italy about an hour north of Milan that has lots of the charm of the southern Alps, and amazing lake and island resort scene, all at much more reasonable prices than just a few miles north over the border in Switzerland.
That time of year should be gorgeous!