What you are saying is so sad. My in-laws were not frum, but they were so respectful of us, and so proud of their son for becoming religiously observant and marrying a frum girl.
I think you should try to sit down and have a “family” conference type talk with them. Your wife should not have to have her yom tov or Shabbos farshterred because of mean-spirited or simply ignorant comments, no matter WHO is making them. But this should be done in as respectful a manner as possible. Maybe it would help to write the FIL a letter.