Some other reasons to say that the Machine is better:
Finch killed and rebuilt the Machine multiple times, and taught it by sitting down and talking to it when it showed "personality traits" that went against his morals: when it lied for personal gain, when it tried to kill its maker to escape its confines, when it didn't show preference for one person if probabilities of success are bad, when and other morals and logic stuff, etc. Presumably, Samaritan's maker (Finch's friend from MIT, whatshisface, of course I can't remember his name) didn't give Samaritan the same amount of attention to morals. It wasn't really whatshisface's fault, he wasn't entirely there mentally. Plus, even if he was mentally there, who was to say he had the same set of moral standards that Finch did? He could have programmed it to go in the completely opposite direction as Finch's machine did.
If I remember correctly, Samaritan required massive amounts of power, which was an obstacle that Finch's machine never came across. Perhaps it was just that Finch solved the energy problem of his machine first, but it seemed morals and kindness seemed to be a bigger problem for The Machine at first compared to Samaritan's power problem. So if I guess right, Finch's machine is more efficient than Samaritan power-wise.
Samaritan seems to not think for itself entirely yet; it still waits for humans to tell it what to do. Then when a human gives it a command, it would cut the human element out of the decision-making on how to carry out those commands. The Machine, on the other hand, while it takes some input from people, it seems to be able to give itself its own commands, and not only that, create its own identity and hire outside humans to follow The Machine's commands, instead of the other way around (it created a billionaire identity and hired a bunch of people to re-type its memory back into itself so it could remember even though it kept forgetting). Not only that, when using its preprogrammed objective (to find people in danger), it still included the human element in the decision-making; it just pointed in a general direction to look, but it let Finch and gang to decide what to do with that information.
There are probably more reasons why the Machine is a superior AI, but I can't think of them off the top of my head.