Can you elaborate? I feel that I've written tests for controllers with Mocha several times without much hassle. Maybe you and I are using the word "controller" slightly differently, or are controlling different things?
If you set up your controllers so that they are independent from the routes, then they are just as easy to test.
It could be as simple as: app.get('/users/:id', userController.userPage). You can then test userController.userPage(req, res, next) instead of the route.