These are my headcanons for what the boggarts of various characters in the Fantastic Beasts movies are.
Credence Barebone - Mary Lou Barebone. Yes, even years later, after Paris and Nurmengard.
Chastity Barebone: Mary Lou Barebone
Modesty Barebone - Mary Lou Barebone
Mary Lou Barebone - the stereotypical caricature of a witch
Newt Scamander - The world inside his suitcase destroyed, with all of his creatures dead (I imagine that his worst fear of having to work in an office changed, since his job wandering the wilds and finding different magical creatures is pretty much the opposite of that, and he worries what will happen to his animals if it's decided they're too dangerous and his suitcase is taken away, like at MACUSA that one time).
Leta's was already shown.
Theseus Scamander - Newt dead or injured.
Yusuf Kama - his father telling him that he failed to avenge his mother.
I couldn't think of anything for Tina, Queenie, or Jacob.