The primary reason for opting for PCI-e over PCI for peripherals other than a video card (or hardware raid controller) is almost solely to phase out PCI, it'll take PCI-e 2.0 and 3.0 to make the standard x1 PCI-e slots head and shoulders superior to PCI.
Choose based on what slots you have available and where you want to place the card, performance shouldn't be any different, especially considering the cards you mention contain only 1 HD tuner. Another thing to consider is that PCI is being phased out, so a PCI-e card should be compatible with a potential future system no longer containing PCI slots.