There are two cases.
If it would have been better somewhere else but is acceptable here, don't close it at all.
If it's off-topic here because it's really not about Ubuntu, then use the "not about Ubuntu" sub-reason under off-topic. As minerz209 says, the correct site (if there is one) doesn't have to be listed in the description of the "not about Ubuntu" reason, for that reason to be used. It's a catch-all for questions that aren't about Ubuntu.
If you're sure it's not about Ubuntu but think it would be unclear to others (the OP or other members of the community such as close reviewers), you can post a comment explaining why you believe it's off-topic and should be closed.
In Respect the community – your own, and others’, Shog9 explains about how one should not close otherwise on-topic questions just because they'd be better somewhere else:
Respecting your own community
As members of a community, your first loyalty should be to that
community. When evaluating a question, you shouldn’t be looking to
push it off on some other site; instead, ask if it could be
appropriate and on-topic for you, the experts who the author decided
to ask. Be a bit jealous of your site – don’t blithely turn askers
away simply because their question could be asked somewhere else.
Don’t hit them over the head with your scope, help them tailor their
question to fit into it – and if that means your site’s scope overlaps
a bit with another site’s, so be it.
Obviously, there are questions you’ll have to turn away, either
because their only connection to your site is via the audience (“How
do I make bread as a programmer?”), because it’s completely
off-topic (“How do I cook a fish in a dishwasher?” obviously belongs
on Cooking, not Home Improvement) or because they’re simply not useful
or constructive. But that should be your last resort. Close questions
with an eye toward improvement and re-opening, not driving users
(emphasis in original)