Very open question, as such no right or wrong answer to this. A USB dongle can be moved from one PC to another with ease, you will be limited to USB speeds though (only an issue with USB 1.x). A PCI card often comes with an external antenna connection and this can be vital if you need to run an antenna away from the PC/a dead spot, put simply i've yet to see a dongle that supports an external antenna (they may well exist).
So in short it depends on what you want to do, what the signal is like in the room the PC will be in and if you want to move the dongle from one PC to another.