Render Controller, what is the best way?

I have an external data source which I would like to output to specific node types. I would now (as I am familiar with Symfony) write a controller which accesses and prepares the data and calls it in the template. Unfortunately I didn’t find any information about the best way in Neos or how to call the controller in the template.

And how can I make sure that the areas are not cached?

I did that very often. So usually I use either an Eel helper or a custom FlowQuery to access the data in Fusion. When further querying is needed I also use FlowQuery for that.
You can then do anything you want with the data in Fusion and also defined the caching behaviour like you would usually do with any other component.

The custom Eel helper or FlowQuery would then use a custom service class that retrieves the data you need based on some input parameters for example.
I highly recommend to the the input data so you can handle problems with the remote api.
I also recommend to at least do a bit of caching in Fusion so your page rendering is not slowed down too much.