In Paradise Regained, the Son is tempted by Satan with promises of worldly power. Through his rejection of Satan's promises, the Son comes to greater self-knowledge regarding his purpose as the messiah. He is not unmoved by temptation or doubt, showing his humanity, but he ultimately triumphs over these struggles, seeking only to obey the will of God.
Samson is a more flawed character than the Son. By the starting point of Samson Agonistes, he is captured by the Philistines and blinded. However, he realizes his loss of physical prowess is not nearly as grave as his spiritual blindness, which led him to become proud and be seduced by the treacherous Dalila.
The one thing these two characters have in common is that they illustrate God's grace in action. The Son is the physical incarnation of God (though not coeternal with God, as in keeping with Milton's unconventional view of the Holy Trinity), so he becomes grace personified by destroying evil and saving mankind. Samson is a flawed human being, but he comes to repent of his wrongdoing and prays to become God's vessel, thus allowing God to redeem him.
Both also stand strong against temptation. Samson is tempted with a comfortable life of childlike dependence with Dalila and then his own father Manoa. The Son is tempted by power from Satan. However, both of these characters have such a strong sense of purpose that they will not waver from their missions.
And yet, the biggest difference between them tying into their internal motivations are the courses they take to fulfilling obedience to God. The Son submits to the will of the Father, subjecting himself to be killed gruesomely in order to redeem mankind. Samson ends up pulling down the Temple of Dagon, killing everyone inside.
Scholars have debated whether or not the Christian Milton approves of Samson's final violent act—does this redeem him or has he only sought to cleanse himself through decidedly unloving means contrary to the will of God? Through these differences, Milton might have been trying to draw contrasts between Old Testament and New Testament ideas of justice, preferring the latter as being more God-sanctioned.