The important factor here is how much horsepower/torque are you expecting to make and at what RPM?
Any Muncie will work - wide ratio or close ratio. The wide ratio will allow for a rear gear like 3.23 or 3.36 and not have to slip the clutch a lot on take off. Using a close ratio trans can make these gears tough when taking off in first gear and especially on an incline at a stop light. Could you still use them? Sure if you don't mind slipping the clutch more and shortening its life considerably.
So with a close ratio Muncie, M-21 or M-22, you would want at least a 3.55 rear gear.
It then becomes a matter of cost, from the lower end for the wide ratio M-20 to the higher side for the close ratio M-21, to the pricey close ratio M-22 "Rock Crusher" - of which was a low production number and highly desireable for those who want original.
The M-20/M-21 Muncie will handle a good amount of abuse, but it is not designed to handle high HP/TQ if you build an engine bigger than stock numbers. That's why the M-22. It will handle more HP/TQ, but again, up to a point.
The aftermarket M-22 design that is advertised on the internet is designed to handle big HP/TQ as it was redesigned in those areas found to be "weak." However, it is not inexpensive.
Along with adding more HP/TQ, you have to address the rest of the driveline. The stock 10-bolt rear won't handle the combination abuse of high HP/TQ, wide tires, and drag race starts. So a rear axle upgrade is needed - however you choose to go.
With the rear axle upgrade, you will need to do suspension upgrades. The stock suspension leaves a little to be desired. As mentioned - wheel hop. Wheel hop can be very violent and break rear ends & transmissions. So this has to be addressed so the wheel hop is eliminated and traction is added. Again, several ways of dong this.
With all that said, it is difficult for anyone here to throw out a simple answer to you without having all the information needed. I would first build the engine, either on paper or actually build it and run it on a dyno. Once you know the engine's HP/TQ and RPM range, then you can select a transmission type and gear ratio to work with the engine. Otherwise, you are asking people to guess/assume on what you want and that never works in real life.