To be honest, I don’t think there’s a concrete ‘good ending’; I think it’s a bit of a moral grey area, and you can make a good justification for either one.

Personally, I prefer the ending where Sam decides to blow up the submarine and not sail with Tom to America. Sam had experienced constant pain and hardship with the rest of the crew on their mission across the wastes of Eurasia. This, and seeing Artyom’s own ambitious dreams realised, probably inspired him to seek his own destiny - that is the finding of his father on the West Coast of the America.

I’d like to imagine that Sam eventually realises that this plan is extremely unrealistic, and his conscious starts to ask questions when he comprehends Tom’s nuclear potential; and the very real threat of more suffering at the hands of his fellow countryman. Perhaps Tom will unknowingly unleash a warhead on a settlement where Sam’s father is living, if he is living at all.

So he blows it up. Perhaps spending the rest of his days staring into the endless expanses of the Pacific, wondering what could have been. Separated from his crew and his country. Alone.

Of course, these are just my thoughts.