CMOS General Input Output (IO) pin speed specification of cyclone IV

You can connect that sort of signal to any of the I/O banks. Best design practice will recommend that you power that bank from a 3.3V supply as well.

The bigger question is - what do you want to do with that CMOS signal. If you do nothing with it the device will quite happily 'operate' at 125MHz.

Assuming it is a clock with which you intend to drive logic, then if that logic becomes complicated the device may not meet timing and therefore may not run correctly at 125MHz.

The slowest speed grade Cyclone IV devices will quite happily drive well designed logic at 125MHz.