The short answer is that SCRYPT has additional protections against brute forcing AND uses PBKDF2. However, which is best ultimately depends on which implementation is most secure for the longest time and only time will tell.
This answer on the Cisco Support Forums provides a comprehensive answer:
Type-8 passwords are what type-4 were meant to be: PBKDF2
(Password-Based Key Derivation Function 2) with 20000 iterations of
SHA-256. While good, this is still vulnerable to brute-forcing since
SHA-256 is easy to implement VERY fast in ASICS or graphics cards.
That is not to say its easy, and in fact if you choose good passwords
it is close to impossible, but it is doable
Type 9: Type 9 passwords use the scrypt algorithm from the
crypto-currency guys. Its whole goal is to ensure that it is expensive
to run the algorithm. It does this first by being hard to run in
parallel and by requiring a tradeoff: Either use lots of memory and be
fast or a little memory and be slow. The trick there is that ASICS and
graphics cards don't have enough memory (memory BW) to run fast so in
practice it is VERY SLOW to run this algorithm. The other interesting
thing is that inside the algorithm is....Lots of PBKDF2 so in Scrypt
you combine the best of both.
Bottom line: Either one of these is WAY more secure then type 5's and
almost infinity more secure then the horrible broken type 4's.