Scenic train ride from Basel to Lake Como?

The most scenic would be via Chur and Tirano over the Bernina Pass. That would take about 9 hours getting you to Varenna on Lake Como, which is a good location.
Faster, but also with good scenery, would be via Zurich or Luzern to Como over the Gotthard Pass. Como itself is not the best location, but from there you can get a bus or lake ferry to other spots like Bellagio. You can also take this train to Lugano and get a bus to Mennagio. This would be about 5 hours.
This should give you 2 full days on the lake. Of all the locations, Varenna gives the easiest way to Milan with a direct train. You did not say which airport in Milan you are using.

ed,

The only one that comes to mind would be something like this.....

• 7 Sept - Travel by train from Basel to Chur (time 2H:19M via direct train). Book a hotel for the night.
• 8 Sept. - Travel to Tirano via the scenic Bernina Express (reservations required). The only departure with the Panorama cars is at 08:32, arriving Tirano at 12:45. However there are also numerous departures of "regular" trains on that route. When you arrive in Tirano, buy a ticket to Varenna-Esino. You should be able to connect with a departure at 13:08 but if not, the next departure is at 15:08. Travel time will be 1H:28M. DON'T FORGET to validate your ticket prior to boarding the train to Varenna, or you'll risk a hefty fine!!! Book a hotel in Varenna for the nights of 8 & 9 Sept.
• 9 Sept. - Tour Varenna, day trip to Bellagio by ferry (~20 minutes each way).
• 10 Sept. - As your flight departure isn't until "the night of the 10th", I'd take a chance and travel to Milan on the day of your flight. Travel to Milan at whatever time is convenient. You can buy your rail tickets for that trip either at the same time you purchase for the Tirano-Varenna segment, or at the helpful Tivano Tours office in Varenna. Again, DON'T forget to validate prior to boarding the train on the day of travel. When you arrive in Milan, you could perhaps store your luggage in the Deposito Bagagli in the station and then have a look around. It would also be a good idea to buy your ticket for the trip to the airport via the Malpensa Express. Buying from one of the Kiosks is the easiest solution (watch your luggage while you're distracted at the Kiosk, or it might "disappear"). The trip from Milano Centrale to Malpensa airport is ~52 mintues. As I recall, departures are from track (Binario) 1 or 2, which are located in an "offset" part of the station.

Thank you so much for the tips!
Btw, I am leaving out of Malpensa Airport (MXP).