In USB, what is the difference between a PHY and a transceiver?
The terminology is vague at best.  There are no hard and fast rules, and nobody playing police when people don't use the term correctly.

Usually, but not always, a transceiver is a simple buffer that has different signal standards on the inputs and outputs.  For example, an RS-232 transceiver usually interfaces TTL signals to RS-232 signals.  Also, transceivers are similar to "drivers" and "receivers" except that a transceiver usually does both driver and receiver functions in the same chip.  

A Phy is similar to a transceiver in that there is usually different signal standards on "both sides of the chip".  With Ethernet it is MII/GMII/etc on one side and, well, Ethernet on the other.  There are other Phy's that talk USB, PCIe, and many others.  Phys usually incorporate some sort of SERDES (SERializer-DESerializer) function and line encoding.  More sophisticated PHYs contain a mini-DSP in them to do all sorts of crazy communication things like advanced baseband wander correction.

A transceiver does not have to be associated with a serial data-- they can be used for parallel data as well.  A PHY usually involves some sort of serial data stream.  But this is more of a convention than a rule, and I am sure there are chips out there that are exceptions to this.