High bandwidth data transfer between hps and fpga

The On Chip memory in the FPGA is just a Avalon Memory component - in theory, you can replace this with another component (including your own custom component)

I'm not sure if the OS is hindering the transfer rate (could be due to various other reasons as well) - as you can see from the example above, you may want to consider using DMA in the FPGA to help speed things up. If you are letting the processor to do all the copying of the data, it may slow things down due to overheads, etc.

Are you performing the transfer from HPS --> (your custom Qsys component)?