Not a lot of difference.
In-body AF is generally nosier. But Some AF_D lenses are very quite, and some in-lens motors are very noisy (not all of them are ultrasonic, some Tamrons are far nosier than good Nikon AF-D lenses)
In-lens AF may be less reliable long term because if the in-len motor fails you might not be able to get it repaired (early generation USM and AF_S lenses cannot be repaired as the parts are no longer made). If an in-body motor fails then you either need the body repaired but at least new bodies for the foreseeable future will be backwards compatible, at least with Nikon.
In-Lens focusing is more expensive as you have to add new motors to each lens.
In-body focus system depend a lot on the body for speed- A pro Nikon D3/4 will focus faster than an old Nikon D70. With AF-S lenses there are also differences, new pro bodies are faster due to faster sensing and processing.
Speed and accuracy wise there is not much difference. Some people will claim the in-lens solution like USM and AF-S are faster, but that is in general wrong. Many of the older screw riven lenses focus faster than the ore modern USM/AF-S lenses.
Accuracy is product of Af sensor calibration, lens element alignment and calibration. Where the motor is that drives the system has no bearing on the accuracy.
You often see newer Nikon lenses with in-lens motors (AF-S) that are much better reviewed than the older AF-D lenses but this is down to image quality and not AF. many AF-D lenses are lighting fast.