I hot tanked my 603 intake manifold with no problem, although it used a solvent which is a petroleum based liquid (and "banned" in some places!)
You don't want to use a strong alkali on aluminum (ie. oven cleaner).
I also used some engine degreaser that is a citrus based stuff available from Granger's
http://www.grainger.com/Grainger/productdetail.jsp?xi=xi&ItemId=1611757438&ccitem=
Neither the hot tank or the spray-on citrus stuff completely removed all of the gunk, I had to use a rag wrapped around long nosed (11 inch) pliers to scrub the stuff off with carb cleaner (toluene based stinky stuff!).
I doubt there is much gain in air flow characteristics from a squeaky clean manifold but it's nice to know you can see the base metal when reassembling a manifold onto a rebuilt engine.