I'd say the Transformer Prime, simply because of the nvidia Tegra2 chip. And the fact that n64 emulators run natively on android while you'd need to jailbreak your Ipad3.
The only iOS n64 emulator I know of is n64iPhone... Which last time I checked has horrible game compatibility and speed. The dev always claims he'll get an update out but they don't happen for months. N64oid on the other hand runs most of my ROMS at full or playable speeds on my HP TouchPad overclocked to 1.7Ghz. Android actually has two different n64 emulators, n64oid (which can be found here: http://slideme.org/application/n64oid) and a free, open source one called mupen64plus AE. ( Which can be found here: http://www.paulscode...8793&topic=96.0 )
I personally use n64oid since it has better performance for me. Grab mupen64plus if you aren't willing to pay/pirate n64oid.