Which Airport in Milan is the best to fly into?

Linate is close in to Milan and there are buses to Milano Centrale station, and taxis are not too expensive.
But re hotel on Lake Como. Where? There are also trains to the city of Como water front from Cadorna station in Milan.
Malpensa has frequent trains to Milano Centrale, but they cost 13 EUR per person and take an hour.

Lake Como is 56 sq miles in area with 100 miles of shoreline.

Just where are you planning to be by 5 PM?
I suspect your departure time is more relevant than which airport, but your destination ( whatever that is) would of course also be a factor.

Hard to know which is the better airport to use, with the info given

We flew in to Linate from London, took the bus to Milano Centrale and then the train to Varenna, Lake Como. I think the train trip was around an hour.

We arrived in Milan at 12.30 but I had pre-booked the 4.30 train to allow for flight delays, collecting our luggage and getting from the airport to the train station. We ended up with time to spare, but it meant there was no rushing and little chance of missing any connection.

You haven’t mentioned where you’re staying at Lake Como. Varenna is easy to get to. Look at the Trenitalia timetable to work out which train to catch to arrive by 5.00.

If you’re staying in another town on the lake, then you’ll have to factor in a ferry trip from Varenna. The ferry is a 10 minute walk downhill from the train station.

No need to prebook trains as these are regional. If you prebook, then I believe you are tied to a specific train.

That correct Karen. We prebooked so we could sit in the equivalent of first class as we knew there would definitely be space to keep our luggage with us.