As I said, I don't know of any microcontroller with PCIe. Someone else may, but I kind of doubt that exists.
I think someone gave you interface ICs that you could add to some MCU to give you PCIe access. I've never used any, and most of those seem to be chinese parts with no docs in English? Dunno.
spostma mentioned fully-assembled SBCs. Doesn't look like what you're looking for. Besides, they would support PCIe host but not peripheral, AFAIK. The SOCs on those boards are very far from microcontrollers. They are SOCs, that usually require signing with your blood (and promise of 100s of thousands of parts a year) for the vendor to give you access to documentation and SDKs, if you ever wanted to develop your own boards with them.
Of course, one option you have it to use a soft core on a mid-range FPGA. Many mid-range FPGAs support PCIe and have ample resources for embedding a decent soft core at a reasonable price. ($20-$40?)
In any case, define "cheap"?
Unless you make 100k+ products a year, nothing giving you PCIe support will be "cheap". But give us a price range.
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