mkfs.fat(8) has the options
-S for custom cluster and sector sizes.
Specify the number of disk sectors per cluster. Must be a power of 2, i.e. 1, 2, 4, 8, ... 128.
Specify the number of bytes per logical sector. Must be a power of 2 and greater than or equal to 512, i.e. 512, 1024, 2048, 4096, 8192, 16384, or 32768.
So the command you want should be something like with the correct device name, 128 clusters per sector and a sectors size of 512byes:
mkfs.vfat -s 128 -S 512 /dev/name
for this purpose vfat and fat are probably the same although the 3DS might only want to read filesystems from partitions marked as vfat rather than fat. fat is from the msdos era and vfat is from the win95 onwards era.