Bookshelf is running on top of Knex.js, so I suppose you can use its migration features:

https://github.com/tgriesser/knex/blob/master/bin/readme.md

There is also a Grunt plugin:

https://npmjs.org/package/grunt-knex-migrate

I've used node-db-migrate (https://github.com/kunklejr/node-db-migrate) on some toy projects in conjunction with Bookshelf, and it seemed to work fine. I haven't used it in production, though.