You can buy PCIe risers, which are basically connectors on each end of a wired ribbon. I'm sure you'd be able to get one to fit under the heatsink (you probably need to remover the graphics card to install it). But you will still need to find somewhere to mount the wifi adapter.
BTW, what's wrong with USB wifi adapters? They come in many sizes and types from a small units not much bigger than the USB port, to units that sit on the desk with a couple of antennas stick out.....they often get a better signal than the PCIe type.