What zone?
MM.111 is said to be a good apple rootstock for heavy soil. The Geneva rootstocks are also tested for crown and root rot but the released rootstocks are more dwarfing than most want for wildlife plantings.
Depending on how harsh your winters are, pacific crabapple (Malus Fusca) could work as a planting or rootstock. It grows along creeks and wet areas on the west coast. That is fairly temperate climate though. Depending on the source, I mostly see Fusca rated to zone 6 or 5. An Oregon nursery, Raintree, sells them as rootstock for fairly cheap. You could plant and tube or cage and see if they survive a few years and then graft.
But if you want to ensure success, I think NH gave you the best option of creating a mound for a high spot.