I HATE HATE HATE the 3DS version it was a cash grab and will NEVER amount to the rovolutionary N64 version that we all know and love.
The OP is asking which you prefer, as in which version you think is a more enjoyable game. I would rather not factor in how great a title was for its time when discussing which version is superior in my opinion today. The question is, however, which do you prefer, so I guess it could just mean personal preference, regardless of the advancement of technology. If I had the choice to have either one or the other, I would choose the 3DS version just because it was specifically built from the ground up to be a bigger, better version of the original.
Having played the N64 version but not the 3DS, I'm not in the strongest position to comment on the subject, but the obvious choice should be Ocarina of Time 3D. Fans may level the argument that OoT for the N64 was revolutionary and mind-boggling for its time, it has been eclipsed by genuinely better games (including Zelda) over the past 14 years.
OoT 3D features the visuals that Nintendo intended for the original to have, and even gives Master Quest an update. The control scheme is simplified but probably not as comfortable, but the sheer amount of revisions and improvements combined with the inclusion of a completely remastered Master Quest is enough to get me on board the 3DS train.