N64 pro's:
Original version
Cheap
Other N64 games can be played on said N64
Glitches and bugs in LoF
oT
N64 con's:
Not portable
Won't hook up to many modern TV's
Takes up space
Dead platform
Glitches and bugs in LoF
oT
3DS pro's:
Portable
Superior graphics
3D
Comes w/ a bunch of other software (web browser, AR games, Mii Plaza, etc)
Glitches and bugs in LoF
oT fixed
New glitches and bugs in LoF
oT
New, growing platform
Z targeting via motion controls is great
Free CD (I got one anyway)
3DS con's:
Not the original - Minor differences that almost no one will notice or care about
Doesn't play other N64 games (Star Fox should be out soon though)
Will tempt you to buy new games and thus empty your wallet
Smaller screen (unless you have a really tiny TV)
Z targeting via motion controls in public makes you look like you're having a seizure (you don't have to use it though)
Glitches and bugs in LoF
oT fixed
New glitches and bugs in LoF
oT
If you want to play the original, I'd grab a Super Joy Box, a PS2 controller and PJ64 and play it emulated on the PC... Not buy an N64. BUy the real cart if you don't want to resort to piracy.
OTOH, I'd still recommend the 3DS option. It's superior in almost every way for LoF
oT, IMO. It's not a dead platform. It's portable. And a host of other reasons that I won't go into.