Help! Koh Samui or Boracay?

Without the 3 year old I would pick Boracay over Samui any day. Boracay however is not a large island and for a 3 year old you have more scope for entertainment on Samui. Beach is nicer on Boracay - blindingly white - but that alone is unlikely to suffice for a 3 year old.
Loads of other options in SEA but depends on your other interests.

Ah, Boracay... the Koh Lipe of the Philippines. Stunning, though now grossly overdeveloped for such a small place. I'd agree with FCIG - Samui is probably more kid friendly. And the Thais love children.

OP have you considered Bali ? far more to do there than Samui or Boracay.
As a 3 year old Waterboom park is something he'll never forget.

For God's sake, FCIG - don't start telling people about Bali. If you don't keep places secret, they end up going the way of Samui and Boracay.

You won't be doing big adventures with a 3yo. If you want a relaxing time I'd go somewhere quiter like Ko Chang. You can do an elephant ride - that would give a 3yo a thrill

I don't have any kids, so don't shoot me for this. But what exactly does a 3 yo actually want to do ? Do they even know where they are?

Boracay does have a beautiful beach, but has become more and more popular, so much so that on my last visit I vowed never to return. Another option if you did choose the Philippines would be Bantayan Island North of Cebu, nice beaches, lots of resorts, very child friendly, but not the volume of tourists that will be on Boracay at Xmas..

Moziebite, Bali (Kuta) is a prime example on how not to develop. Hardly a secret place anymore.

3yos like animals - they would love an elephant ride. otherwise they would be happy to play with a sand bucket on a beach. if you take them shopping they want lollies.