This is a good problem to have, both locations are great for sightseeing. I don't know either hotel but have stayed close to both.
Assuming the hotels themselves are equally good for your purposes, I'd give the edge to the Latin Quarter. Closer to more Metro and RER options, plus the wonderful Luxembourg Gardens (but don't miss the Place des Vosges). Probably more dining choices nearby, though there are plenty in both areas. Rue des Ecoles and Rue de Rivoli are both busy streets, but as I recall Ecoles is a little wider and has more trees. These are subtle distinctions, to be sure. That's why your "problem" is a good one. You really can't go wrong with either location.
With luggage, I'd recommend a taxi from Gare du Nord to either location. You'll probably pay a little more to get to the Latin Quarter. Or you could RER "B" to Chatelet (for Marais) or St-Michel (for LQ), in which case the walk or taxi will be longer to the Marais place than to the LQ place. You could shorten the walk and avoid a taxi by taking the Metro to Hotel de Ville (Marais) or Maubert Mutualite (LQ), with the shorter walk at the LQ location. But these logistical differences are minor, shouldn't really determine where you'll spend six nights.
Both neighborhoods have plenty of cafes, and I think you and your daughter will find both safe and comfortable. Both will have lots of people around at night. In fact, I'd suggest you try for a room up high and/or facing the back to keep street noise from disturbing your sleep.
Yes, the Atmospheres is downhill from the Pantheon (well worth seeing close up, but overrated inside imho).