Arria II Power Supplies - Switcher or Linear?

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Yes, there are analog circuits on the PCB board as well, and we are really concerned about noise in this application because of the analog circuits associated with the application.

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Ok. Then analyze the FPGA power requirements and see if they can be met by linear supplies. If the FPGA needs to use a switcher, then you will need to pay attention to layout.

If your analog section can use differential signalling, then that will improve the common-mode rejection of any switching signals.

Micrel have a range of switcher noise suppression linear regulators; basically active filters acting as low-dropout regulators. You might be able to use those to cut down the noise from the digital section of the board.

Cheers,

Dave