I don't think anything in the Tufte-LaTeX document classes would
affect \numberwithin. It looks like it's not defined. You might
double-check that you've included \usepackage{amsmath} prior to the
block of code you provided above.
If you still have problems with this, could you send me a complete
example (from \documentclass to \end{document}) that illustrates the
problem?
Thanks!
--Kevin