Which transmissions would mount up directly to my 64 malibu crossmember?

Lots. What are you interested in? The PowerGlide Th350, TH400, TH200R4 and TH700R4 can all fit.

Im just looking at my options automatic or manual transmission will all of the later muncie models fit as well?

Yes, the M20, M21, and Saginaw will all fit. The M22 might need the crossmember to be moved back or possibly some additional brackets welded onto the frame.