I'm currently using a wireless controller because it's the only one I have, but if I could get to choose again I'd go with a wired one.
First of all, I still have to plug in a Bluetooth adapter to use it, so it's still taking up a USB port. Second, I only use it to play PC games, so even a wire wouldn't pose that much of a problem (although I'll admit that being free of hindrances is fine). However, I'd rather get to recharge my controller with a dock or something rather than constantly replacing batteries, since I don't always have them at hand.