problem 1: your cooler is too noisy
problem 2: how to turn it off when shut the sistem down
answer 1: I use a 12v 0,04a 4x4cm cooler, is very silent. I know the rpi just boost 5v, but it works perfectly.
answer 2: I set up a system to turn on and off (acording the led should be on/off).
You have to use a transistor to work as a on off switch. So you have to conect a gpio pin that is reserved to put a LED at your transistor. When the gpio pin put 3,3v to the "LED" you use it to switch your transistor on and freely the 5v passage to the cooler, and vice versa.
1) buy a pnp transistor (i use bc558b) (my friend said to use a fet transistor)
2) conect the base of the transistor at the GPIO14
3) conect the another pin of transistor at the 5v cooler gpio
4) conect the another pin of transistor at 5v entrance of your cooler
6) conect the ground wire of your cooler at graund
7) took off your sd card and conect to your PC
8) open the config file at notepad++ and erase ;
at begining line "system.power.switch=PIN356ONOFFRESET"
take a look here
queria responder em português mas acho q a gringarada vai ficar no horror haha boa sorte