The difference between the two that sets them apart is the KIT, not the supercharger itself.

A Magnacharger is a complete SYSTEM with far fewer shortcomings than a Whipple kit.

Magnacharger Pros:
- Customer Service
- Complete system
- Intercooler
- 8 larger injectors
- Tuner included
- Replaces troublesome stock manifold that has #7 AFR problems with boost

Magnacharger cons:
- Price
- Supercharger efficiency

Whipple Pros:
- Superior compressor technology (efficiency)
- Price

Whipple Cons:
- No intercooler
- Does not replace stock injectors
- Auxiliary EFI computer with auxiliary injectors
- Pulley upgrades limited by drive hub diameter
- Stock intake not designed to be "wet" but this kit makes it so

There are probably a few more minor items that can be added to all four of those catagories.

Personally, I am a Whipple fan because of how much better screws work than roots rotors. Twin Screws are real compressors. It's been a hotly debated topic in the past here because there are so many die-hard Eaton fans. In order to get out of one the performance levels the compressor is really capable of providing, you have to build your own system from scratch with it or buy the ultra-expensive "off-road" Gen III/IV kit.