I am not aware of a direct train from Malpensa to Lake Como. You can go from the airport to Como with a change of trains in Saronno. You can also go to Varenna in the mid-lake area with a train change in Milan. You say you are going to Lake Como, but where on the lake? Como and Varenna are the towns on Lake Como with train stations. To get to other towns on the lake you will need to take the ferry.
Because there is no direct train service between Malpensa and Lake Como the train is not the most ideal way to get there. I would either rent a car and drive there or hire a driver to take you.