With oiiotool you can use
--colorconfig /path/to/config.ocio
to specify a OCIO config. You could then point it to the "aces_1.0.3/config.ocio" that ships with Nuke, or download the "aces_1.0.3" dir from the OpenColorIO-Configs GitHub repo and point to the config in there.
Alternatively you can set your system "OCIO" environment variable to the config path prior to running your command, which is what OCIO uses by default.
Then it's just a matter of giving oiiotool the correct color space names to use from that config, for example:
oiiotool --colorconfig /path/to/aces_1.0.3/config.ocio -i [source.exr] --iscolorspace acescg --tocolorspace logc3ei800_alexawide -o [dest.dpx]
If you're using the same config as what you're using in Nuke, you can use the same color space names you have set in knobs (i.e. match the Read node "colorspace" knob value; with surrounding quotes if the name has spaces).
Hope that helps,
Mike