Creating a Zynq boot.bin has been a source of headaches for quite some time. It requires a toolchain different from the one in NDK build and also seems to have some dependences on variations of other common Unix tools.
The only reason anyone has to build a boot.bin themselves is because it contains the MAC address for the ethernet. On the zedboard, at least, there is not a better place to store it. Zybo does have an eeprom for this purpose, but we do not have that working yet.
I'm working on a web-hosted development environment, and as part of that took a step towards packaging zynq-boot in an easier to use way.
I packaged the stable, board-independent pieces into sdcard-zynq.zip and the faster changing or board-dependent components into bootbin-$(BOARD)-$(MACADDR).zip. If you only have one board of a particular type, you can use a prebuilt bootbin.zip. Otherwise, you'll still need to be able to build boot.bin or to use the web-hosted boot.bin creation service when it's available.
The current prebuilt images for zedboard, zc702, and zc706 are here:
Best regards,
Jamey