I use both at different times, and I have not done anything special. In fact my computer is probably pretty messed up :-)
Open the NII sdk shell and then the file that points to... make sure that it can find bash - that all the pointers are correct.
tell me if that helps. If it doesn't we'll see if we can find something else.
maybe???? did you install Quartus in a different location AFTER you installed Nios II? I don't think this should matter because it looks for Q home dir..
And how are you invoking the shell.