Two Arduino boards - one IDE
That's the way to do it.

You need to select the type of board first:



And then the port. You can have both devices connected at the time and select which one you want to program.



With Arduino you can do OTA (Over The Air uploads) to NodeMCU and other ESP8266 based systems.

If you want to run two instances of the IDE, to work with two different boards at the same time, use UECIDE.