For what it's worth, the NAIA also has their own NAIA Eligibility Center and the cost is the same $90 ($150 for international athletes at both NCAA and NAIA).
Also, as FoxDad said, registering with the NCAA Eligibility Center isn't required to play JUCO ball. However, I usually recommend registering while in HS even if the athlete knows they're going to start off at a JUCO.
Knowing whether your athlete is a Qualifier, Academic Redshirt/Partial Qualifier, or Non-Qualifier will allow your athlete to know what academic requirements they'll need to satisfy while attending the JUCO in order to be eligible when they transfer to a D1 or D2 program. (And if you're not confident that the JUCO coaches or advisers know what those NCAA academic requirements are, that's a good time to contact Informed Athlete for that detailed information.)