Max Gpio mhz for cyclone II, III, IV ?

The FPGA itself is certainly capable of such speeds, but you won't be able to reach it by controlling the SSD in software and PIOs. You will need a dedicated controller with DMA support, such as this one (http://www.cast-inc.com/ip-cores/storage/ataif/cast_ataif-a.pdf).

I built a PIC18f based system that controlled a compact flash using GPIO, The cyclone III has a end GPIO of about 250 MHZ from digging around the internet, I think this would be best for my project, what do you think ?

I Want to control a PATA SSD with it at high speeds (over 60 megabytes a second)

If you are talking about a PIO on a system with a Nios CPU it depends on many factors, mostly the CPU type, its frequency, the memory type and interface connected to the CPU instruction master port, the amount of cache and the kind of software environment you will build your application upon.

Hopefully I am asking the right question and not been sold a bill of goods to upsale me, my experience is limited to PIC proccessing but I am looking for the right proccessor with alot of speed in the gpio area.