As far as I know, the clock speed for ISA slots was between 7MHz and 8MHz. On the other hand, PCI is 33MHz. That said, I don't think that you will see a huge difference in printing performance. I would still get a PCI interface though because they are 1- easier to find and 2- probably cheaper.
I dont know that I would go as far as replacing the Mainboard, unless you were looking to upgrade anyway. I am assuming, since you said that USB is an option, that you have USB on your PC?