why dont you use nios2gcc-20080203.tar.bz2 from
http://www.alterawiki.com/wiki/binarytoolchain then
tar jxf nios2gcc.tar.bz2 -C /
The cross gcc tools was expected to be installed in /opt/nios2 dir. But you may install in any other dirs. Then setup the PATH for the cross gcc, you can add a line at the end of file ~/.bash_profile (or ~/.profile on Debian/Ubuntu) ( the file is hidden, you have to use "ls -a" to find it . For "gedit" use open Location, and enter the file name)
PATH=$PATH:/opt/nios2/bin
I did this my compiler working fine