The Vierne Berceuse used to be a favorite, but it has a sad history. The Adagio from his 4th Symphony is a gorgeous piece.
I wouldn't dream of picking a "best"...
One piece that does come to mind: the Prélude in B major, by Fleury (it is part of the 24 pieces for harmonium or organ). The piece is luminous.
I too, have a soft spot for Franck's Prière and Barié's Lamento, and the opening of his Symphony.
Duruflé's larger works are stunningly beautiful.
I'm moved by the works of Achille Philip, but have not had much luck finding the music.
Franck's Trois Chorals are probably closest to the pinnacle, for me.
Widor's Romane (heard live at St-Sulpice) left me quite speechless. I have a favorite recording of it that has the same effect. Odd, since I usually find Widor to be a bit austere.
Then there is Bach, Howells, much of Whitlock; Rachmaninoff's Vocalise, Barber's Adagio, Sowerby's Symphony. Some of these are 'beautiful' in a soul-stirring way, not necessarily because they are pretty.
(And so forth...)
Soubasse32