Both have advantages and disadvantages.
With a camera body, that has internal motor, you can use a lot more lens with autofocus - any AF lens, not only AF-S. And these AF (but not AF-S) lens are (often) much cheaper than lens with built-in motor.
For example, you could check the prices of 50/1.8 AF-D and AF-S. Or 70-300 AF and AF-S (+VR).
Example for body with AF motor is D7000.
The bodies without internal motor can autofocus only with AF-S lens, obviously.
An advantage of AF-S lens over AF (but not AF-S) lens is the speed: AF-S lens can focus faster. And this is really important for wildlife/sport photography.
Another advantage is the availability to use autofocus on bodies without internal AF motor, of course (for example, D5000/D5100/D3000/D3100/etc).
But this is not always true. As far as I know (but never used them), the Nikkor 300/4 AF does not focus slower than the Nikkor 300/2.8 AF-S.