In the Latin Quarter we totally loved Hotel des Grandes Ecoles in Rue du Cardinal Lemoine. It books up far ahead of time so it may not be available on your dates, but the neighborhood is super. You can walk down to the Ile de la Cite and Ile St-Louis in 10-15 min (more like 15-20 min coming back uphill), and in other directions you have the Pantheon, Musee Cluny, Natural History Museum and Jardin des Plantes, etc. It is also a great neighborhood for food; we especially liked the bistro La Contrescarpe and the restaurant Le Volcan.
You might call Hotel des Grandes Ecoles even if they are full, and ask if there is a comparable hotel nearby that they would recommend.