Milan Hotel

I enjoyed my stay at Hotel Garda which is near Milano Centrale Station.

Hotel Berna, across the street from Hotel Garda, is also a popular hotel with this forum.

Have a wonderful trip!

Hotel Garda! Completely agree! Stayed there once, amazing experience

Hotel Berna on Via Napo Torriano, which is located about 400 meters in front of Stazione Centrale. The property is extremely clean, the staff is first-rate, and they serve the best breakfast in the city. We have stayed there many, many times.

Buon viaggio,

We were at Hotel Berna just this week, leaving Italy, and I agree with the above input. I would definitely use this hotel again: comfortable beds, bathrobes, free drinks in the mini-bar, great service, location, & breakfast.
Enjoy Lake Como; I miss the area already!

The two hotels mentioned in previous replies, Hotel Berna and Hotel Garda, are both only about a five minute walk to Milano Centrale (I know as I've timed it) so either would be a good choice.

One question though..... is there a reason you're not going to Lago di Como right after arrival? Where are you staying on the lake? It's only about a one hour train ride from Milan to Varenna, so very easy. I've found that it's so much nicer to suffer jet lag a bit longer and then be able to wake up to the tranquil beauty of a place like Varenna on my first full morning in Italy.

Regarding going straight through to Lake Como on the same day:
[ just last week,] we found those trains, each way, to be packed, like city buses, and had to stand throughout one route. I would find standing for an hour, when being incredibly jet-lagged, to be very difficult.
Safe travels!

I would recommend Hotel Berna, I stayed for two nights and then took the train to Varenna on Lake Como for a RS Best of Italy tour. 5 minute walk from the Centraal station. Clean, comfortable room and helpful staff. Easy walk to restaurants nearby.

There are direct trains from Malpensa airport to Como city, every two hours. Times here: http://www.tilo.ch/dam/jcr:bf8e7297-1ad1-4534-800a-def910357833/COSG_VAR_MXP_12.2018-6.2019_web.pdf
Travel time 1.5 hours or so.
If it works for your plane arrival, then you can spend that first night in Como.
If the above schedule does not work, you can also take a Malpensa Express train to Saronno and change there for Como. I don't see the need to backtrack to Milan if you do not plan to visit Milan that day.

Stayed at the Hotel Michelangelo. Think it's more business oriented but nice and close to Milano Centrale.