I agree with Tim - Our family of five stayed in the Hotel Excelsior Latin last summer. Our kids/young adults are similar in age to yours - we ended up with a two room suite with a wall but not a door between the two rooms. We thought the bathroom, deluxe shower and separate tub were especially great! This was for four nights, offered AC which was essential in the heat wave we endured in July, and had a great location. The street was quiet, but just a very short walk to the Boulevard Saint Michel, and the location was wonderful. We went to Maison Pradier every morning for their "breakfast formule" - which was excellent every time. We also discovered that this patisserie won the top eclair in Paris 2015 award, so of course we tried them, as well. (14 Boulevard Saint-Michel, 75006 ) There was a Marks and Spencer nearby, which made for easy picnic choices. (35 Boulevard Saint-Michel)
We were near Luxembourg Gardens, the Cluny Museum, the Pantheon, the Sorbonne, Notre Dame, and all sorts of great stores to browse and food choices to enjoy.
I did a lot of looking into apartments, and in the end, decided that the predictability of an established hotel was way less stressful than a potential apartment crackdown problem. Another time, and perhaps if it was just the parents, we might make a different choice, but this worked out well for us.
Hope this helps!
Laurie