MathJax 3 currently only supports the default font, as more general font support is still under development [1]. According to the relevant GitHub issue, font support is planned to be part of the next major release, which is supposed to arrive sometime this year [2]. This should then include Gyre Pagella out of the box (as was the case for MathJax 2), but also make it possible to use custom fonts (which apparently wasn’t possible with MathJax 2) [3].
[1]: http://docs.mathjax.org/en/latest/output/fonts.html [2]: https://github.com/mathjax/MathJax/issues/2503#issuecomment-... [3]: https://github.com/mathjax/MathJax/issues/2503#issuecomment-...