Quartus II: Suppress warnings by Verilog module
You can right click on a warning message, then go to "suppress", then choose between various "quick" suppress options or pop open the Message Suppression Manager that allows you to visualize, edit, import and export all the rules you want.

As OP says in the comments below you can also use the * wildcard, so to suppress all pcie messages he wrote *pcie* and that did the trick.