What are the differences between Altera & Xilinx Deserialization?

What device and speed are you running at?

In general, use Altera't True LVDS I/O when possible. This is pretty close to dedicated silicon for running high-speed interfaces. TimeQuest will report an RSKM value, which you need to determine if it's fast enough for your system. If you want a really fast receiver(up to 1.6 Gbps), then you'll need DPA. Probably the biggest downside to Altera's solution is that it's not as flexible, being dedicated silicon. For example, you may not have enough I/Os. Or you may run out of PLLs(although DPA can help with this too.)

Xilinx has some dedicated features in each I/O, which tends to make their solution more flexible. It's basically a calibrated delay chain and serdes function. The downside is that for higher clock rates, it takes logic to control all this. Look at their real-time window monitoring.

For the most part, you should be able to do anything in both architectures, so I wouldn't worry so much about comparing the two.