That depends on what you're presenting.
If you're presenting the low level animation and experience, then you have to do it in the medium of the final product. Anything else is either a poor approximation or unimplementable. You would never present how a paper will fold or how its texture felt on hand or its subtle scent on a screen, why would you try to present how a button do hover effects on paper?
If you are presenting the high level interaction between users and the components, you can't feasibly build them without having spend a huge amount of time building it, so you need a stand in. Also, high level presentation done on the actual medium might give the false impression that you're nearly done or that you are already set on low level details that aren't actually the main topic for the current presentation, which is the high level interaction. A sketchy presentation would communicate the high level overview without overwhelming the client with the details.
Also important is that when you're presenting low level animation details is that you should put them in the context they're used in. So if you're presenting a menu bar, frame them in with the rest of the pages, when presenting a hover effect, present them as they'll be used in a form. Do take care to deemphasize those contextual elements so people can focus on the current point (e.g. mute their colors, use generic, neutral images, use lorem ipsum texts, etc).
Presenting these animation in the final medium will also allow you to do feasability study at the same time. Nothing is worse than promising a very awesome design your client just LOVE in After Effects, only to end up not actually being able to deliver them as they're just not possible in the medium.