Paris in 7hrs

Since you will be taking the train, you will arrive at Gare du Nord in Paris. The train to Milan probably leaves from a different station. If you see Eiffel Tower and Notre Dame Cathedral you may have time for a meal and to wander on over to Ile St. Louis for a stroll and ice cream. Take a taxi to Gare de Lyon for your train to Milan. Allow plenty of time as that train station is very large and can be confusing.

I'd go to the Louvre or D'Orsay. I bet your boys would love to visit the Catacombs.

A Pedi cab or a boat between the Eiffel Tower and Notre Dame would be neat for the boys.

Where will your luggage be if your train leaves from a different station? Make sure you have time to drop off/retrieve it.

http://joinusinfrance.com/layover-in-paris-episode-73-2/

A one-hour boat cruises give you a fun view. The Bateaux Parisiens brand travels roundtrip from/to their dock near the Eiffel Tower: http://www.bateauxparisiens.com/static/BP/plan-croisiere/plan-croisiere-big.jpg

With a high stakes time constraint like this one, I'd be cautious about doing the Catacombs, because you never know how long the line is going to be (it can be an hour and a half); and once you're down in there, you're committed and don't have the ability to end your tour early in case you're running late for your train.
And then there's the possible delays of rush hour to the station if you take surface transportation.

You would need to allow approx 2 hours (to be sure) for getting back to Gare du Nord, collect luggage and get to Gare de Lyon for your Milan train. How's this time line ??
00:00 Store bags at Gare du Nord, then get RER B to St Michel for Notre Dame.
01:30 Then RER C to Champ de Mars for Eiffel Tower.
03:00 Then Metro line 6 (green) from Bir Hakeim to Etoile for Arc de Triomphe + Champs Elysees
04:30 Take Metro line 2 (blue) from Etoile to Barbes Rochechouart for Gare du Nord
05:00 Collect luggage, then take RER D from Gare du Nord to Gare de Lyon and your Milan train
07:00 Milan train departs Gare de Lyon

Why not let each of the kids choose one place they want to see and let them do a bit of the research and planning. If you get to see more, it will be a bonus, but 2 important sites that they boys are invested in would be really special. Plus, let them help figure out the logistics, etc.

Thank you for all the wonderful suggestions! My only concern now is storing our luggage at Gare du Nord. Anyone done that before? Do I have to worry about the lockers being full when we arrive around 1pm?

From the man in seat 61 ...

The Gare du Nord has left luggage lockers ('consigne automatique' in French), open 06:15 to 23:15 daily. The locker area is located downstairs under the main concourse opposite platform 3 - when you walk off the end of the Eurostar platforms onto the concourse, look for downward stairs just ahead and to the right of you. All your bags (even those you're not leaving) are X-rayed before entering the locker area as a security check. A small locker costs €5.50 for up to 48 hours and will take a medium-sized backpack. A medium locker costs €7.50 and might take 2 medium backpacks. A large locker (around 1 metre high) costs €9.50 and will take a large suitcase or 2 large backpacks. No keys are involved, you shut your locker, pay the money and a receipt is printed showing a code for opening the locker. There's are change machines which (if they're working!) can convert €10, €20 or €50 banknotes into the coins needed for the lockers.

I know it´s not in the centre of Paris, but if the boys like airplanes you can consider going to the Aviation and Space Travel Museum of Le Bourget Airport. It takes 16min. by RER train from Gare du Nord to the RER station of Le Bourget and think about the same additional time with the bus or taxi from there to the airport.

I don't know when you will be traveling but the day we wanted to check our bags at Gare du Nord the baggage area was full. We had to wait in a line with approximately 10 people ahead of us. We needed a large locker and we're just lucky when our turn came a group of American college students came in and vacated theirs! Our wait was well over an hour so plan your time accordingly. We were there in October.

Oh well, if the lockers are full just have your boys sit on the cases (no doubt with iPads) and tell them to wait until your return. lol