The Binding of Isaac: Rebirth has been confirmed for Xbox One, Wii U and New 3DS. But not the older models of 3DS (i.e. 3DS XL, 2DS, and regular vanilla 3DS).
The announcement was originally made by the game's creator, Edmund McMillen, on the official The Binding of Isaac site, but it went up on 1st April and McMillen made a lot of jokes about how he was censoring the game to fit Nintendo's family-friendly sensibilities. Things like changing god into a dog, adding a leaf to Isaac's groin, and recalibrating all the Christian imagery to satirise Scientology instead. But in the cold light of 2nd April he and Tyron Rodriguez, who's handling the ports at Nicalis, have clarified that the game is in fact coming to the aforementioned platforms and "is not censored in any way."
Rodriguez credited Nintendo's former indie game chief Dan Adelman for getting the darkly comic action-roguelike on Nintendo platforms. "If one (former) Nintendo employee deserves all the credit for Isaac Rebirth on Nintendo consoles, it's based @Dan_Adelman," Rodriguez tweeted.
When asked about prior 3DS models, McMillen told Eurogamer, "We simply couldn't get the game running well enough on the old system and weren't going to release a subpar version."
No release window has been announced, but McMillen said these console ports should be out "soonish." Here's a Vine of the New 3DS version in action.