like a few people have said, i would just get an emulator, but you can also get drivers for a ps3 and 360 controllers (just google it!) so you can beat that problem, then if you have a notebook/laptop like i do, i got a s-video cable/hdmi cable and ported the picture from my laptop to my tv, and ta-da you now have a ps3/360 controller playing old n64 games on a tv
If you dont have a corded xbox 360 controller or a ps3 controller, then get the 360 controller, because nearly all 360 controllers are wireless now and it will be cheaper also ps3 remotes are like $100 if you live in australia like me and the cords are not as long (pfft only play-asia for me from now on, lol) also the s-video cable i got was $1 on ebay (a hdmi will prolly be about 10 to 15 on ebay but alot better quality)
If you wanna keep the feeling you can get a N64 retro port (changes the n64 cable into a usb cable) but i would advise against it as the N64 controller are just not as well desgined or made
I also found that the frame rate, colour and smoothness of the graphics were alot better through emulator (AND IT IS FREE)
Hope this helps make your mind up