

32kb is a good choice for compatibility.
for more details:
Bigger unit (cluster size) will speed the read access as the files are less fragmented, but you will loose more space if you store a lot of file smaller than 32k : Each used unit can only store one file, so if your file is 33k it will use 2 unit with 31k lost space. It will also let you format bigger HDD size (up to 8TB in FAT32).
Smaller unit will prevent loosing space, but will create more fragments after intensive deletes/writes, making HDD file's seeking slower. you need to defragment the drive if it happens.
HDD : 32k, for most homebrew it's the best choice. If you want to use DIOS MIOS it's the maximum supported allocation unit size with HDD. I think it has also better compatibility with Wii games, but I can't confirm that.
SD : 64k is fine, and will speed up reading speed if you use DIOS MIOS Lite. But anything bellow is working too. 64k will loose even more space than 32k if you store small files (covers, cheat codes, etc.)
it depends if your main purpose is to play gamecube games from SD or not.
I use 32k for SD card and the speed is just fine for both gamecube and triforce games.