What are your boys into?
Food is always on the mind of teens, a food tour is always a hit.
Are they active, play lots of sports, bicycling around the city or, parks is one way to burn off the excess energy that teens have. Get up on the roof of the Milan Cathedral.
Are they into fashion/street vibes? If there's one thing that'll get rid of the boredom for teens....it's hanging out and being around other teens.
Are they more introverted or, into gadgets, perhaps spending some time at the Museo Della Scienza e Della Tecnologia (National Museum of Science & Technology), not only do they have interesting contemporary exhibits but, a whole area dedicated to the ideas and inventions of Leonardo da Vinci.
You have three boys, one of them is bound to be bored while the others are fired-up about something, you know your kids best, their interests and what they're capable of. . Probably best to get them involved in the planning process, you don't need to get them into every aspect but, you can certainly layout some choices or, give them a list of places to check out and allow them to research it. As for some water/beach time, halfway in-between Milan and Venice is Lake Garda, lots of interesting towns around the lake, a stunning bike path that sits above the lake is instagram worthy (if your boys are into posting) and there's Gardaland. Arguably Italy's best theme park for rollercoasters and themed attractions, sort of Disney but, not really.