When arriving at EWR you need to reclaim your luggage and hand it in again, yes. This happens after immigration. You will also need to re-enter security. In other words, there is no way to get to any lounge on arrival, but only after you are back in the 'safe zone' again.

In the C-terminal there is a continental lounge with nice showers. I used them a few weeks back. Do you know if the EWR-ATL flight leaves from the C-terminal? If so, just locate the Presidents Club right on the other side of security to get a shower.