As you wrote best way is catch the train from MILANO STAZIONE CENTRALE to VARENNA. It takes 50 minutes.
Then spend some time to visit Varenna that is nice village.
There is a nice walk from the ferry to the historic centre.
And you can visit Villa Monastero, or Villa Cipressi.
Then catch the ferry to BELLAGIO.
It takes 15 minutes and the ride is very panoramic.
Once in Bellagio you can explore the historic centre. Unfortunately the garden of Villa Melzi will reopen on the 26th.
From Bellagio to Como you can catch the BUS (50 minutes) but it is not panoramic.
Otherwise you can catch the fast boat "hydrofoil" to Como.
It takes 50 minutes and you can see other nice villages along the lakeside and nice villas.
Another nice villa that will be open is Villa Carlotta in Tremezzo that will reopen on the 15th.
Once in COMO you can catch the train to MILANO.
Hope this helps. Brezza