You could make use of git log and set it to only return the top most commit:

RevCommit latestCommit = new Git(repository).
   log().
   setMaxCount(1).
   call().
   iterator().
   next();

String latestCommitHash = latestCommit.getName();

Compare by dates of last commits in all branches. ListMode.ALL can be changed to ListMode.REMOTE to compare only remote branches. Or... the fluent setter .setListMode(whatever) can be omitted to read from the local repository.

RevCommit youngestCommit = null;
Git git = new Git(repository);
List<Ref> branches = git.branchList().setListMode(ListMode.ALL).call();
try {
    RevWalk walk = new RevWalk(git.getRepository());
    for(Ref branch : branches) {
        RevCommit commit = walk.parseCommit(branch.getObjectId());
        if(youngestCommit == null || commit.getAuthorIdent().getWhen().compareTo(
           youngestCommit.getAuthorIdent().getWhen()) > 0)
           youngestCommit = commit;
    }
} catch (...)

To find the newest commit within a repository, configure a RevWalk to start from all known refs and sort it descending by commit date. For example:

Repository repo = ...
try( RevWalk revWalk = new RevWalk( repo ) ) {
  revWalk.sort( RevSort.COMMIT_TIME_DESC );
  Map<String, Ref> allRefs = repo.getRefDatabase().getRefs( RefDatabase.ALL );
  for( Ref ref : allRefs.values() ) {
    RevCommit commit = revWalk.parseCommit( ref.getLeaf().getObjectId() );
    revWalk.markStart( commit );
  }
  RevCommit newestCommit = revWalk.next();
}

Depending on your use case, you may also want to mark start points from refs from repo.getRefDatabase().getAdditionalRefs() which includes refs like FETCH_RESULT, ORIG_HEAD, etc. If you find that there are still untracked refs, use repo.getRefDatabase().getRef().