For the heatsink, the Hyper 212 is a good HSF. However, I like the Scythe Mugen 2 Rev. B a lot more. It offers a lot better cooling for only $10 more.
I don't believe there are any internal readers with USB 3.0 headers. I don't even think USB 3.0 motherboards have USB 3.0 headers that it would connect to. I'd probably just buy a regular internal card reader (most have a few USB slots, plus room for different flash cards, and maybe firewire and eSATA) for about $15-20.