FAT file systems are FASTER then NTFS mainly because FAT systems don't have the overhead in which NTFS has, such as security permissions, indexing etc. However with today's super fast

HDs, the difference in speed becomes less noticable and to be quite honest, with my new HD, I can barely notice the difference in speed between FAT and NTFS.
In my opinion, go for NTFS unless you are still using other Operating Systems, it is defintely a better file system.