First of all, why is there algae in your loop? Your using distilled water right?
There are certain products made to kill algae, just make sure the stuff doesnt contain chlorine or something else that dissolves plastic. Either that or isopropyl alcohol. Or you could blast the loop with UVC light, that would kill everything in both the loop and the pc. UVC light ages plastic though, and you would definitely want to be out of the room went the light is on.
I used pc-ice. When it got a little low I filled it with my roommates distilled water he uses for his humador. It must have gotten something in it though because it exploded almost overnight.
I haven't had any problem killing it... I submerged all my crap in 99% isopropynol and I'm pretty sure that killed it all. Now I'm looking for something to remove it. algae is a tough bastard when it's in a radiator.