The out-of-the-box Nios-II software development tools will work just fine.
You can download u-boot at:
http://www.sourceforge.net/projects/u-boot (
http://www.sourceforge.net/projects/u-boot) (multi-platform/official site)
or
http://www.psyent.com/download (
http://www.psyent.com/download) (Nios-II only)
Note that the main source tree tends to lag significantly behind the
psyent site (it's a big project so things move a bit slower). The psyent
site also includes a few "nips & tucks" to ensure a warning-free
build in the Nios-II cygwin environment.
Regards,
--Scott