Uhhh. Neither?
Both are relatively... antiquated technologies. ISDN never really caught on (here) and Frame-Relay is fading fast. There are a couple Frame-Relay providers are not doing any new installations.
That said, if you are being forced to use one of these protocols, personally, I would go with Frame-Relay. And the only reason for that is I think it's easier to implement and troubleshoot than ISDN.
One advantage that ISDN has over Frame-Relay is that it's a point-to-point circuit switched protocol. Which means that when the link is up, it's like a T1 (or fractional T1). The downside is that it's typically much more expensive that Frame-Relay.