Synthesis NIOS II source files by Leonardo

Nios II is synthesizable using Quartus II only, sorry!

...there are a lot of reasons for this. Originally Nios I was synthesized with Leonardo. A couple of years ago Quartus native synthesis was greatly improved and we got the same (if not better results) using Quartus. This continues with Nios-II today, which has been hand-optimized in many ways to target Altera devices & use the Quartus II native synthesis.

Please note that you can synthesize your own logic using Leonardo, for example if you create a custom peripheral or custom instruction and import it into your SOPC Builder system, the relevant wizards allow you to import a netlist.