pteam, Google is working on new 301 code according to Matt Cutts blog:
I would not risk another redirect for any reason so I would just place a link to the new site and 404 all the pages.
marty98, if you are running ASP I might have some code for you on my personal site that would be of help... sticky mail me for the URL. To answer you question however I don't think either method is safer than the other but consider 301'ing a single page at a time would only effect that page. Again, it appears Google is working on new 301 code so Iwould wait until that is in place before doing anything else.