The rebound from Voldemort's final curse.
As Deleteman states in the comments, when Harry first sees the house, he guesses that the damage was caused by a backfiring spell:
Most of the cottage was still standing, though entirely covered in dark ivy and snow, but the right side of the top floor had been blown apart; that, Harry was sure, was where the curse had backfired.
This guess is correct.
When Voldemort tries to kill Harry, the damage is near immediate: as he comes to terms with his ethereal state, he sees the damage to the house:
And then he broke. He was nothing, nothing but pain and terror, and he must hide himself, not here in the rubble of the ruined house, where the child was trapped screaming, but far away... far away..."
Voldemort's spells are described as very deliberate. This isn't a duel; he's not casting lots of spells, but a few carefully targeted shots. The first two spells he cast were to kill James and Lily, not to attack the house. Indeed, it's not until Voldemort's wand is pointing at Harry that he realises that something is wrong; if the house was already blown apart, he'd work it out a lot sooner. (The noise of the explosion, if nothing else.)
This means that when he tries to kill Harry, the house is still intact. It follows that it must have been the curse trying to kill Harry, because that's the only spell from which the damage could occur.