Zigbee kind of feels like it's in a weird place right now. Some of the better consumer grade zigbee products have REST APIs that are easy to learn and you can get the job done with the built in websocket node (I do this with DeCONZ.) Others, like philips hue, have dedicated nodes available that make interacting with the zigbee coordinator much simpler from the node-RED side of things (I'm a fan of huemagic here.) I've also worked with medical grade zigbee systems that tend to revolve a lot more around SQL queries to drive the operation of their server.
There's a lot of reading and experimenting out there to do, and "best" is a judgment that relies so much on context that it sort of begs the question: "Well, what do you want to do?"