As other wrote, the weather in lake distric in sept. and october is variable so that unpredictable. Anyway I wouldn't go there later than October because the weather and lots of restaurants, holel and shops close. Moreover also some palace/gardens close (i.e. Borromeo palace and garden on the Borromeo's islands in the Maggiore lake).

Still from 15 Sept.you'll find far less tourists because the start of schools.

Here some web site about lakes district: http://www.lagodigarda.it/ http://www.lakegarda.com/ http://www.lagodicomo.com/ http://www.lagomaggiore.com/

To schedule your ferry trip: http://www.navigazionelaghi.it/

Enjoy the lake district,

Marco in Milan - Italy