That's right J636 - the fact that flights have the same number doesn't mean that it's a through flight. For example, our AA55 MAN-ORD also happens to be the same flight number as a later ORD-LAS service, operated by a different aircraft. US carriers have duplicated flight numbers for decades, possibly because they would run out of numbers otherwise.
And anyway, even if it were the same aircraft all pax would have to get off at the first point of entry to the US and clear immigration there.
And even a cursory check of the JFK-BOS leg for AA211 shows it as being operated by a 738....