The boost packages are slotted, so you can actually have more than one version installed.
To emerge that version, simply issue:
emerge -a =dev-libs/boost-1.39.0
If you want to remove the newer version (quite dangerous, you could have a lot of stuff dependent on it), you could:
emerge --unmerge =dev-libs/boost-1.46.1-r1
and run a `revdep-rebuild` afterwards.
To switch your environment from one version to the other (if you kept both), use `eselect boost list/set`.