ocarina of time 3D was better in my opinion because it had much better graphics. but thats not the only reason though, i dont like judging games only on graphics.
its better because, well... you could take the adventure with you. because i own a lot of console games that i really love, but can only play when im home. but because OoT is on the 3DS now, i dont have to worry about one of those games anymore! (now all i need it super mario galaxy, majoras mask, and kirby on the 3DS...)
another thing was is that i love all the patterns that games have on certain things inside them. like, i love colorful games that have a lot of design in them. and the original OoT on the 64 had very dull colors. the 3DS one though, its like theres color everywhere, and i love it!
Ocarina of Time 3D is obviously a remake of the N64 original. The 1998 original was more revolutionary but the 3DS remake is better simply due to added features like the boss battle mode, Sheikah Stones, gyroscope controls, as well as updates graphics not to mention portability.
The 3DS version is better for the portability, improved graphics, superior controls, and additional content. The only advantage the N64 has is if you prefer playing games on a big screen and/or want to have an audience as you play it. The 3DS is hands-down my preferred version.