Are you refering tot he NTFS Allocation Unit size when formatting the NTFS volume from a Windows FORMAT perspective?
If so, you can choose whatever Allocation Unit size that the applciation recommends. The underlying Nimble Volume will use a 4KB block size when using the default ESX 5 Performance Policy, the allocation unit size does not affect this setting - but should always be the same or larger that the underlying Volume block size.
A good example of this is for a non virtualised NTFS Volume being used for SQL Databases (DB files), The Nimble Performance Policy for SQL would use an 8KB block size (this matches the SQL Paging size perfectly but the NTFS Allocation Unit size is recommended by MS to be 64KB.
A good explanation of this can be found in InfoSight: https://in.nimblestorage.com/twiki/pub/Support/ProperBlockAlignmentForNimbleKB/Proper_Block_Alignment_for_Nimble_KB.pdf