Long answer:
The PS3 won't accept your NTFS drive because NTFS is licensed by Microsoft and Sony doesn't want to pay for a license. Most likely they don't want to take the time to build an NTFS driver for their system either. Because of the way files are stored on a harddrive (FAT uses, as the acronym says, a single table to allocate the space for the files, NTFS is more dynamic in this), FAT will be slower when you have a large number of files on a disk. This information doesn't help at all though as the PS3 will still not accept an NTFS drive

Although there are tools to repartition a drive and make the unused space into a separate FAT32 partition, all of those tools are notoriously dangerous and may (in a significant number of cases!) destroy the data you have on it. My advice would be to simply backup all of those files and reformat the drive completely. This may, however, be a challenge as most Windows versions don't allow you to format a FAT partition if it's over a certain size.
Short answer:
Backup your files and re-format the drive. You may need to use the DOS command for this:
format /FS:FAT32 X:
(where X: is the drive name)