There are valid reasons for identifying Eva as an especially moral character, but I would choose Tom as the novel's most moral character.
Admittedly, the child Eva has an angelic purity of spirit and faith that causes her to treat enslaved and free people with the same kindness and respect. Eva's deep faith and innate moral goodness cause all the slaves to love her. She has a beneficial effect on the entire household, except perhaps on her selfish mother. Eva, laying on her deathbed, admonishes everyone in the household to be good to one another.
However, Eva never has to undergo the pain, suffering, or moral challenges that Uncle Tom does. She is born privileged and pampered and dies in a state of innocence. Tom is the more moral of the two because he is continually tested, facing down evil at great cost to himself.
Tom hates being enslaved and would give almost anything to be free—except his moral values. He puts the needs of other people first. He could, like Eliza, run away rather than face the bitter horror of being sold away from his home and family. However, he knows the others who are enslaved will suffer and be sold instead of him if he runs, and he refuses to do that to them.
Tom faces his biggest moral test when he is bought by the evil and depraved Simon Legree. Tom could save himself by becoming an overseer and oppressing the others enslaved there, but he refuses to compromise his soul by hurting others. Instead, he accepts death at Legree's hand. He becomes a Christ-like figure, sacrificing himself for the sake of a larger good.