They do still serve cream puffs (Napolians) at Les Halles ... still as good as ever.
Note that they also dish up a nice Troll Horn (cream horn) and School Bread (cream custard filled pastry) over at Kringla in Norway. I think I actually prefer school bread overall.
When you asked about a cream puff, I was thinking more about the traditional type: a profiterole (roundish pastry with whip cream or ice cream filling). The Napoleon (which is yummy) is layers of puff pastry alternating with cream. Similar ingredients, but very different texture (to me).
In that case, I would recommend heading over to the Kringla (Norway pavillion). They have a berry cream puff, which is basically a cream puff with mixed berries added. I saw a photo of it in a review on the Disney Tourist Blog from February so it was still there at that point. It looks the same from March of 2013 (when I was last there).