Do a search for guestappartment in paris. I had a great rental from them with a Seine view.

One I stayed at is the Notre Dame (now called St Michel). We had top floor loft...our view was sunrise over Notre Dame and the Seine...and all of the night views of the cathedral lit up, boats on Seine,etc..Location was optimal, with RER station to airport across the street, lots restaurants,etc..
Noise was not an issue. Have not been in several years, Tripadvisor seems to like it.

http://www.hotel-paris-notredame.com/


For Ile St Louis, have a look at these (Lutece and Deux Iles):

http://www.paris-hotel-lutece.com/

Jeu de Paume and St Louis are two others to look at. Note that rooms can be small. Jeu de Paume seems like a nice splurge