I am unaware of a single source for the ANV muster rolls. By perusing individual records at Fold3, one can assemble a reasonably accurate muster roll for a number of regiments based on the June 30 pay date (which I have painstakingly done in a few cases). But records of some units covering that period were evidently lost/destroyed (including by Federal cavalry during the retreat and during the burning of Richmond at war's end). A few original rolls survive in repositories like the Library of Virginia in Richmond. A reference work, Regimental Strengths and Losses, by John W. Busey and David G. Martin, offers total numbers for every unit (ANV and AoP) as of June 30. Of course, the latter figures differ from battle strength, given that roughly 15 percent of any given unit's complement consisted of non-combatants in various support roles (and do not account for absences like sickness or desertion).
It is my understanding that AoP muster rolls may reside in the bowels of the Library of Congress, but Fold3 has yet to make them readily accessible. Again, I have seen just a handful of original company rolls that reside in repositories around the country. Also, those figures are sometimes provided in official reports or in post-war accounts by participants.