Have not been to Paris for a few years, but I used to recommend "La Dame Blanche" (47 rue de la Montagne Sainte Genevieve
5), but they seem to have closed doors (or at least their web-site has, staff is very quirky, but selection was very unusual not least if You are in to vinyl), Also the Classical department of
jussieu music (rue Linné) used to be well stocked (and might have closed) and
La Chaumière à Musique (seems to have changed name to "Melomania" @ 38 boulevard Saint Germain) is a place I bought from on-line but never visited, but their stock has always impressed me.
The big
FNAC department stores will still have a good selection, they are a sort of French Amazon (the one on Rue du Terne was well stocked)... Gibert Joseph (Blvd. St. Michel) used to have a large classical department, but I'm not sure about their status!
/ptr