addressing on-chip memory(cyclone IV) from PC via PCIe

It might be worth trying to read/write from one of the simd (SSE3) registers - it is just possible such requests will generate a single PCIe transfer.

You'll need to check whether windows allows kernel code to use them - if not you'll have to disable pre-emption and save/restore the register.

It is rather a shame that the altera PCIe block doesn't contain a dma engine (a simple single transfer one would suffice - scatter-gather could easily be build on top). For Nios code, spinning waiting for completion (in code) would be fine - allowing some overlap but without the cost of termination interrupts.