Trying to remember a book I read in grade school (published prior to 2005). It follows a group of kids that were saved from a nuclear holocaust by being placed in stasis. The mutated man that let them out of stasis is the boys father.
This has a familiar ring.
This could be Flight of the Eagles by Gilbert L. Morris, the first book in the Seven Sleepers series.
The book had some strong christian and anti-semitic tones. The nuclear holocaust had released things from inside the earth and completely changed the geography and people of the Earth. The main villains were the Sanhedrin and the group traveled to various locations, including Atlantis and Camelot, getting help to stop them.