Switzerland in June?

One idea would be round trip (not the usual recommendation) to Milan, followed by a train to Varenna. Take the ferries to Bellagio and other lake towns and hike/explore from there.

Take the train from Varenna to Ticino, then a train (Bernina Express if you want the panoramic views, otherwise regional trains run the same route) to St Moritz, Switzerland. Lovely hiking up there! Take the gondola (or hike) to Piz Nair summit; hike down.

From St Moritz you can take the Palm Express bus (sit on the left side for best views) or trains to Lugano. Again, lots of wonderful hikes! Take the funicular (or hike) to Mt San Salvatore; hike down.

From Lugano, you can either return to Milan, or continue up into Switzerland.

Really, I admit I'm a sucker for water. Canal towns are just beautiful. I just loved Venice so much. The photos of Annecy are something else, but I'd suspect it's only a day or so of activities and sites. I'll add Chamonix to my research! I've not been to France at all, but proximity to this itinerary seemed reasonable.

I've only been to Italy, Ireland, and England thus far as Europe goes. Italy has been my favorite, the small towns in particular.

If you do live in Vermont, you can get a non-stop from Montreal to Zurich.
Skip Interlaken, you are going to Muerren. Easy to get by train to Zermatt and Lugano and back to Zurich airport by train. Hope the weather cooperates.

Thanks @CWsocial I'll check those spots out. I have been to and didn't care for Milan, but it is a easy airport to get in and out of from the northeast and offers close range to Switzerland.

There is amazing hiking in Switzerland! Zermatt, of course, is well worth it if you can hit it during clear weather.
Between Zermatt and Lake Geneve there is an area called Valais. You mentioned that you like water and that's why I'm throwing this out there.
In this region there are ancient waterways called "bisses" that were both dug to bring water from the high alps down to the orchards and vineyards in the valleys below. Some of them are 700 - 800 years old and some of them are more modern. Many of them follow hiking paths and are pretty interesting features that I haven't seen in other place around Europe. Some of the water channels are hand dug in the ground and others are troughs that cling to the side of cliffs and hillsides. You can start in the high mountains with spectacular views and follow them down through the forests to the valley floor.
Here's a link to some of them so you can check them out....
Other than that this region is beautiful with few tourists...Sion is a great town with a castle and ancient church perched on the two hills in the middle of the town. There are castles up and down the valley. Vineyards and orchards. If you want a view with spectacular hiking then Mont Fort is where to go. Not only is the hiking great but it also boasts the highest bar in Europe.

If you want to do some more "virtual hiking" around Murren and surrounding areas, click on my name to find a link to our dozen favorite hikes there, with maps and pics.

@anita great thank you! Sounds like weather in those valleys can be unpredictable. In general, June a good month or a poor month to visit you think?

@shoe, great fantastic site. thank you!

The usual advice is to add a couple of days to your stay in the mountains to increase your odds of good weather. In my case, I was there in early July and had five sunny days ... and I still could have stayed longer without running out of things to do.

I like the idea someone suggested of flying into Milan. I think a first trip of Lugano/Locarno, Lucerne, Jungfraujoch region (I’m a huge fan of Wengen), and finishing in Zurich sounds like a great plan. Bellagio is also beautiful in Lake Como. It really depends on how much time you have. You do not want to race through Switzerland, you want to slowly savor it. I would hold Munich for another trip. And I have only been to Switzerland in the summer (I am not a skier) and it is heaven. (However, bad mountain weather is a very real thing. We were in Zermatt for 3 days and literally saw the Matterhorn for a combined 45 seconds on that trip.)

Thanks for the replies, the weather thing is very good to know. I need to grab the book and get my region learn on. I've liked driving a great deal in Italy, would one suggest car over train for any reason or stick to rails?

Update: Tap Air Portugal had a sale I simply could not say no to. $603 round trip open jaw NYC > Paris then returning to NYC from Zurich 12 nights later (arrive 5th June, depart 17th June)

Now the fun begins, filling in the gaps! Having never been to Paris we'll stay 2 nights and take the fast train to Geneva on the 7th, sleep there.(maybe Lyon?) That seems to be the best bang for the buck. Then we find our way to Annecy for 2 nights (8th, 9th), non-negotiable my lady says.

Then we work our way to Zurich eventually on the 16th. So I have 6 nights I'll need to park ourselves with Switzerland proper. Zermatt is important to me, and somewhere around Interlaken I think.

Exciting!! Thanks for your help thus far!

That is exciting indeed!

Unless you have a reason to stop in Lyon, I recommend you take the high-speed train right to Geneva. The high speed train gets you across France very quickly, and both times I've taken it I felt like I'd barely settled down and then we were there (I haven't taken it to Geneva, but to Bordeaux and Torino). So before you decide to break up that part of the trip that can quickly get you to your original goal (Switzerland, Italian Lakes), think about where you want to spend your 2 weeks. It's nice not switching rooms every night or two (conversely it's really cool to go lots of places).

Alright, Swiss rail pass secured. Hotels secured. All that is left is to wait and continue researching day plans & trips!

From Annecy on Monday the 10th we plan to travel to Zermatt for 2 nights (Phoenix Hotel)
Will then be staying Lauterbrennen for 3 nights (airbnb)
1 night in Lucerne (Hotel Des Alpes)
Last night in Zurich! (Best Western Old Town)