I enjoyed playing it on the 3DS, it's nice to be able to play it wherever and not be tied to the tv. Pausing whenever is convenient too.

I'd say keep it classic and play the original N64 version.

I vote for N64 version since OOT is such a long game, and I honestly HATED playing Majora's Mask on the 3DS XL - it became very uncomfortable for me! I'm likely in the minority but i prefer 3DS games that are not super time intensive, I can't ever find a comfortable way to game it out for hours. I'll take a big screen and a wall of pillows behind me any day!

Try the circle pad pro. It has the same ergonomics as the Wii U gamepad.

I would go for the N64 and that is where I am playing Ocarina now and I love it. I originally played the game on N64 and since then I have played it on the gamcube and on the Wii VC. The thing I forgot about the original was how perfect the controls were with the n64 pad. The Z trigger and the shield feel so natural on that setup and the rumble pak is pretty cool.

I plan on playing Majora's Mask next on the 64 as I only ever played that on the gamecube collection.

Play the original first, then the 3DS. It will give you context and appreciation. If you play 3DS first, you'll never see the original in the same (blocky-ass) light  

3DS, but I've always preferred portability.