Yes, there is USB onboard, since the very first iPhone. There's also been Firewire in the past. Pinout image
Fairly unlikely to be USB3, though, I'd guess it's USB2.
However, it's certain that Apple have made it very difficult to access.
Currently with jailbreaking and the iPad camera connection kit (an adapter which makes the USB pins of the dock connector available via a USB socket) you can only get a USB keyboard to work, you can't use mass storage devices or external devices such as MIDI keyboards or audio interfaces.
It's a shame, really, the USB controller is in there! You're just not allowed to use it. Perhaps in a future iOS update it will be made available.
First the iPhone has always had USB support via it's dock connector. Sorry to say it's limited to the 1.0 or 2.0 spec in speed depending on your model of phone.
The new iPhone 5 now supports USB 2.0/3.0 depending on what you connect to via the new Lightning port.
As to the USB controller is part of a Apple custom chip heres theiFixIt iPhone 3GS teardown Check out step 11 diagram So you really can't swap it out (even in the newer iPhone 4/4S models).
The first gen of iPods had Firewire support then USB was added about the same time the iPhone was introduced and later Firewire support was dropped.