Agree that Musken's TR was great -- I used it to plan our stay.
Eamus FYI, my kids are 12 and 9 years old. They slept on the two daybeds that seem to be part of every casita in the resort; they essentially are twin beds, perhaps slightly narrower, but definitely good for kids as young as yours. We had considered upgrading to one of the villas, but the combination of the significant increased expense (triple the casita cost) and the fact that multi-bedroom villas are configured as individual casitas grouped around a common courtyard/pool area -- which means your kids would be in a casita not adjoining your casita, but rather separated by an outdoor area -- persuaded us to bite the bullet and share a single casita.
There were many kids' activities, especially for younger children like yours; the nanny-to-child ratio was remarkable: when we went to the club to check it out for our younger child, without exaggeration there were at least eight nannies playing with two children. But re kids' activities remember to double-check with Amanpulo before you book, because I suspect that many of the activities disappear during non-school-holiday-break periods.
Totally agree with Musken that Amanpulo is a great place to go with kids, one of the best Amans for that. I think the only one that has been better in that respect is Amanbagh, where the kids rode camels daily (sometimes twice per day), and loved all of the many excursions around the local rural area, including interacting with local children in the village. I suppose the fact that the kids had their own house-sized suite (shared with their grandmother) with its own pool may have added to their enjoyment. It certainly added to ours.
One last (slightly off-topic) point, for which I hope I won't be berated on this Aman thread: the best kids' program we've ever experienced was at the Mandarin Oriental Dhara Devi in Chiang Mai, Thailand. Truly incredible, including riding water buffalo through rice paddies, planting rice, making crafts with locals in a "village" that the MO created on-property. My kids still talk about it years later. And the hotel is great too.