In Orwell's Animal Farm, how does Squealer manage to persuade Boxer and the other animals that Snowball was Jones's agent at the Battle of the...

Squealer was incredibly persuasive and used scare tactics about Jones coming back constantly.

The pigs use Jones as a propaganda technique long after the humans are gone from the farm.  They are constantly reminding the animals about the atrocities of Jones, and telling them that if they do not cooperate, Jones will come back and behave tyrannically as before.

“… Do you know what would happen if we pigs failed in our duty? Jones would come back! Yes, Jones would come back! Surely, comrades," cried Squealer almost pleadingly, skipping from side to side and whisking his tail, "surely there is no one among you who wants to see Jones come back?" (Ch. 3) 

The animals do not want Jones to come back, so they do whatever the pigs say.  They do not complain about the pigs’ abuses, such as taking the milk and apples for themselves.  Whenever the pigs want the animals to stop complaining or to not think too hard about something, they just mention Jones and the matter will drop. 

Connecting Jones to Snowball was easy.  Squealer and the pigs have been telling the other animals that Jones will come back and that the farm is in dire peril.  Now they can claim that Snowball, who opposed Napoleon, was secretly in league with Jones.  It fits perfectly, and the animals believe anything Squealer says, so it is perfect. 

We had thought that Snowball's rebellion was caused simply by his vanity and ambition. But we were wrong, comrades. Do you know what the real reason was? Snowball was in league with Jones from the very start! He was Jones's secret agent all the time. (Ch. 7)

Napoleon slowly tightens his control over the other animals.  In time, his leadership is even more controlling and damaging than that of Jones.  The animals are actually worse off than before.