I'd like to use both cygwin perl and native strawberry perl on the same machine. Because they both find ~/.cpan I think it would make a mess to use them like this, right?

No.

cygwin concept of $HOME is different from windows concept of home , but even if it wasn't, cpan can generally share the same directory without problems.

If for some reason cpan can't, cpanplus can do it

You can configure each install through a custom CPAN::Config installed in site or vendor libs

Can you suggest a clean way to operate cygwin and strawberry dist together, each having separate ~/.cpan and ~/perl5 dir?

Don't keep them both in %PATH%, and don't use MyConfig