I realize this is an old thread, but thought I would comment in case it is helpful for someone else.
If you want to copy from the Nios II Console and then past to a text editor , you can try this to see if it works...
save printf output from nios ii console: • Currently using Eclipse from Quartus Prime 17.0. Not sure if this works in other versions.
• I have not found this documented anywhere, just found it by trial and error.
• Prior to clicking the run button, kill the Nios II Console window if it is open. It will re-open when it starts running.
• During/after run has executed, select text in Nios II Console window.
• Select Ctrl-Insert key combination. It should now be copied to the clipboard.
• Paste with Ctrl-v.
• This only seems to work once. Must kill window and re-run to do another copy/paste.