Staying closer to Malpensa instead of on Lake Como is a cogent strategy. Any number of glitches can occur when transitting a long distance to make a flight. Good thinking.
As for a hotel, we can highly recommend the 4 star Hotel Berna located on Via Napo Torriano 400 meters from Stazione Centrale. The property is outstanding, the staff is exceptional, and they serve the best breakfast in the city. There are a number of good restaurants in the area and you are a short metro or taxi ride from the historic center. We've stayed there many, many times and we are always satisfied.
The Hotel Berna is close to the main train station enabling you to use the train or the bus shuttle to the airport. We've never used the express train because we like the shuttle bus. This past August we used Blacklane Limo service and were happy with the service. Blacklane was more expensive, but it does provide you with another option.
You didn't mention what time of the year you will be traveling, but a great last night spot in Milano is the Navigli District. It is a gentrified warehouse district along canals. The zone is packed with many restaurants, bars, clubs, gelatorie, and it's a fun spot for and after dinner passeggiatta (stroll).
Buon viaggio,