Transportation from Lake Como

Lake Como is a big lake. What town are you staying in?

There are car rental agencies in town of Como, but none in Lake Como (I could not resist that).

We will be staying in Varenna or Como, unless you recommend a more accessible town.

We've visited both Varenna & the town of Como & I'd recommend staying in Varenna.
Varenna is amazingly beautiful & you can easily visit the other mid-lake villages (Bellagio, Menaggio & Lenno) via ferry.

Having said this, it looks like you may have to return to Milan to continue traveling to your next destination(s), especially if you plan to take public transportation.

The town of Stresa, on the shores of Lake Maggiore, is definitely a more accessible town, as traveling to Zermatt or Gimmelwald is more direct, will take less time... and... you will not need to return to Milan.

You may want to check train schedules here: http://www.sbb.ch/en/home.html

Checking above website, it looks like traveling from Stresa to Zermatt will take around 2.5 hours with 1-2 train transfers, depending on what time you choose to travel.
That's not the case when traveling to Gimmelwald, as this will take almost 4 hours with multiple train transfers.

If you choose to stay in Varenna or the town of Como, you will need to return to Milan and you will be traveling 6 -7 hours, depending what time you choose to travel.

Hope this helps!

From Varenna, you can take the ferry across to Menaggio, then a bus to Lugano. From Lugano you could take a train to Luzern, then Interlaken, then on to Gimmelwald.
To Zermatt, take the train at Lugano to Locarno, then to Domodossolo, then to Brig, then to Zermatt, or to Gimmelwald via Spiez and Interlaken.
After all that, you may just decide to head back to Milan and go from there.
I didn't mention the long end-around via Tirano and Chur.