As someone who played both, my personal vote would go to the N64 version.
However, to you specifically, assuming you have played Ocarina of Time, I would advise playing the version that corresponds to the version of OoT you played (if you only played one of them). The familiarity of the screen layout and control scheme is probably going to matter more to you than the version differences.
I agree with most others with regard to the changes made in the 3DS version (good and bad). For me, the bad outweighed the good. OoT 3DS was the superior version largely because it focused on adding instead of changing, such as including the hint system and the boss rush and Master Quest modes, none of which you necessarily had to interact with if you didn't want to.