We've used the Club Saturnin, which is in Meribel itself so you'd have to get your son down to the Chaudanne. There are regular free buses between Meribel and Mottaret or alernatively, you could ski down La Truite with your ds in a back pack - but although it's only a very gentle green run, I'd only do that if you were a confident skier. The only thing about the Club Saturnin is that it only "opens" between 9 and 10 (from memory) and and again between 2 and 2.30 (if you're only using it for half a day)with pick ups between 12 and 12.30 and 4.30 and 5, so you couldn't put the child in late, for example (all the times, as I say, are from memory, but aren't made very clear on the esf web site). I think it's a security mesure, as the creche is upstairs from the entrance, so they lock the door outwith these times. You also need to book in advance.
The Club Saturnin is the esf's (ecole de ski francais) creche for the younger kids - while there is an outside area, they do NOT do ski instruction - CountessDracula, wherever you found that description, it is misleading. But they do have fun in the snow, weather dependent. From THREE, there is the Jardin de P'tits Loups (there's one in Mottaret), where if you provide the child with skis, they will start with some rudiments of ski instruction. But your wee boy will be too young Gizmo.
We put our ds in last year for a couple of days (he was 2 and 4 months) on the Saturdays that we didn't get a nanny supplied. He seemed very happy and well looked after - but he is used to being in a nursery environment.
Best details are here - but as I say, they don't make the fact that you can only drop the kids off and pick them up at certain times very clear.
Kids etc is a new English speaking creche down in Les Allues, but I understand that she will arrange for kids to be picked up around the resort - I presume that means Mottaret as well as Meribel itself. He wouldn't get to play in the snow, as it is unlikely that Les Allues will have any real snow cover.
Mottaret itself is good for playing with kids - plenty of gentle slopes to take them sledging, so you can have fun. You could also take the Plattieres or Pas du Lac bubbles up to the top and meet the "skiing" half for lunch en famille.
I don't know the hotel - we've always stayed in a chalet in Meribel (reminds me - must book, but unfortunately, dh doesn't want to take ds this year, as he thinks it might be our only skiing holiday), but generally the skiing hotels are really flexible, and I'm sure they'll be geared up for kids.