Node.js is a great option for real-time applications, especially in conjunction with Socket.IO.
In terms of databases, I'd go with PostgreSQL. MongoDB has its benefits (schema-less, sharding, map-reduce), but for most CRUD-based apps, it makes sense to store the bulk of your data in a relational database (of which PostgreSQL is the best IMO). You can throw in MongoDB if you have a specific need for it. There's certainly no need to use both MySQL and PostgreSQL.
As for GraphQL, it can be nice to work with since you don't need to predefine specific data endpoints on your backend, instead shifting the power to your frontend in requesting the data it needs. It's also useful for public APIs, when you don't know what data users want (see Github's API). It can be useful at the early stage when you're prototyping and want to be able to fetch data quickly, but certainly isn't necessary.
At BaseDash we use Node.js, ExpressJS, Socket.IO, PostgreSQL, and Sequelize to fit our use case of database management and real-time operations.