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.