So I ve played the n64 for quite sometime and hope to make a handheld of it in the future, would you recommend keeping the original joystick or getting one of those cheap gamecube replacement ones?
I wouldn't recommend either to be honest. If you are using a first party controller, the best option would be to use a micro controller so you can use a high quality 10k joystick. If you are using a 3rd party controller like the super pad, you do not need a micro controller and can simply wire up a joystick normally. In the end, it comes down to your own preference.
You can always use Micro's N64 Stick Converter PCB v3. It's a quality micro controller (as Gman pointed out) with an upgraded joystick, You'll still need a Gamecube style replacement stick to place on top. It's what I'm going to use and I think this would be the best solution.