There is a direct bus, if the times work for you. About 55 min ride.
http://www.safduemila.com/alibus-2017-malpensa.lagomaggiore-1.html
If the bus schedule is not to your liking, the best alternative is the train from Stresa to Gallarate (25 min) then the 10 min taxi ride to the airport, as lachera mentioned. I haven't taken the taxi from Gallarate to MXP in several years, but I remember it was not cheap even then, considering the very short distance. So don't be surprised if the taxi nowadays is 30+ euro for those 10-15 min.
Give them a call or write an email and see what they charge.
http://www.taxigallarate.it
Gallarate has a modern decent size station, and there are always taxis parked in front at the stand. Lots of people from the area take a taxi to the airport from Gallarate.
You could also book a private car transfer (limo) from Stresa all the way to the airport. Convenient and fastest way, but plan on about 90 euro for up to 3 passengers.