We will be passing through on the train to Milan, only for one night. We want to be near the Paris Gare de Lyon station. Nothing too noisy. Doesn't have to be top of the line, but clean, safe and accessible to nice cafes.
There is an Ibis hotel not far from Gare de Lyon.
In 2014 we spent one night at the Ibis Gare de Lyon ledru Rollin because it was a short walk to Gare de Lyon, and we were catching a train there early the next morning. The hotel was perfectly adequate for one night, and I was surprised by how good the breakfast was.
http://www.ibis.com/gb/hotel-1937-ibis-paris-gare-de-lyon-ledru-rollin-12th/index.shtml
Another vote for IBIS.
There's a pretty good Holiday Inn just down the road towards Bastille in an older building with good brekkie and a distant view of the Eye-full Tower from some higher rooms.
I've also stayed at the Mercure right on river side of the station which was fairly good. Convenient, not bad but not memorable. Breakfast room is up some stairs from the lobby or a special lift.
There's also a Novotel right alongside the station. Google Novotel Gare de Lyon. When the Google map comes up, you can zoom in and see all the hotels right around Gare de Lyon.
Novotel is in the same hotel family but a step or two higher up from an Ibis. The Ibis may be perfectly fine for your needs!
http://www.novotel.com/gb/hotel-1735-novotel-paris-gare-de-lyon/index.shtml
We stayed a few nights in the Hotel Corail near the station, found it clean and comfortable and affordable. Our room on a high floor was quiet and there was an elevator. There were plenty of places to eat nearby.