NativeLink is the buzzword Altera uses for the link between Quartus-II and third party tools like Synplicity or ModelSim. It really just means you can operate those tools from within Quartus-II or Quartus from within the other tool. I don't recommend it because you lose some capability of a tool when running it from another. Many people like to do it that way, though.
Avalon is the bus spec used within SOPC Builder and with Nios-II. Most, if not all, cores targeted for Altera parts will be Avalon compliant. There are two types of Avalon: Memory Mapped and Streaming. Avalon Memory Mapped is a pretty standard address/data bus scheme with some DMA capability. Avalon Streaming is an evolution of Altera's Atlantic spec which connects streaming data components together. It's used for things like video and DSP cores.
Hope that helps.
