I am not certified in Kindermusic, nor have my children taken Kindermusic classes, so I'm not really qualified to give you a run-down comparison. The thing that makes them hardest to compare is that one is a curriculum designed for home use and the other is a franchise.
The advantage to doing Kindermusic is that your child would be participating in a classroom setting with other kids, playing ensemble, and interacting with a live teacher. I think there would performance opportunities (mostly just for the parents, but it still gets your foot in the door). The community choir I had my kids enrolled in did, and it was good practice for them. The cons are, you're committed to a specific time and place to get your child to class.
On the other hand, Preschool Prodigies is a curriculum parents can do with their children at home. They can watch the videos again and again any time of the day, every day, once a month, whatever fits your schedule. There is no public performance on the calendar, but there is no commitment requiring you to juggle your schedule either.
I did a little browsing on the Kindermusic website before responding, and it looks like the "Young Child" is designed for 5-7 year-olds, but there are classes for other age groups as well. I looked at their "curriculum solutions" as well, and I caution that those packages are designed for classroom teachers who already have a good idea what they will be doing. It's not a step-by-step, day-by-day curriculum like Preschool Prodigies, but PsP doesn't come with so many physical music toys aside from his package that includes the desk bells.
What it boils down to is deciding whether you want to take your kid to a live class or teach them at home. If you want a live class, you might also look into Suzuki or Yamaha if they are in your area.
Side note- If you do happen to choose Preschool Prodigies, you can get 20% off with the coupon code "TCM", which would also give me a little kick-back.
Good luck! Either choice would be a good one.