My site pr=2 has all pages indexed without the www version .
It is also ranking good for many urls.
Should I redirect naked domain to www one or should i redirect www version to naked one?
Or leave it as it is?
For which one should i build backlinks?

If you already have incoming links to one of them use that and redirect the other to it. In your case it be redirect with-www to non-www

We all know Google is enough smart to figure out the www and non-www versions. It means there is no any content duplication problem. But when it comes on backlinks then Google consider both the version different and thus your link juice is divided in two different ways. Nevertheless previous reply is enough good for you to redirect your www to non-www because your non-www version is good in their position compare to www.

Check the backlinks for both the versions of your site. Also check the cache for both sites and then decide.