I have ran pd on a raspberry controlling it with VNC Viewer over wifi quite successfully. Since I keep editing the Pd project I need to have access to the GUI, but I would prefer run it headless on the rpi since that would free up quite a bit of cpu.

Could you run Pd's GUI on one computer (i.e. my laptop) and Pd audio process headless on another (i.e. the RaspberryPi)? That would be so neat.

@cfry Why it might not help much.....https://lists.puredata.info/pipermail/pd-list/2012-02/094145.html
What happens as Pd connects to the Gui.........https://puredata.info/docs/developer/PdStartupOrder

Command flags........ https://puredata.info/docs/faq/commandline/?searchterm=flags
You will need to start Pd with the -guiport or the -guicmd flags depending on how you will achieve your aim.
There is help mentioned at the bottom of the page for that...... here is a direct link....... https://lists.puredata.info/pipermail/pd-list/2007-08/052604.html ...... but it's not very helpful.

Everything would have to pass through a network connection though...... so I am not sure that things will improve.

If your VNC connection is stable you can edit your patch through the VNC viewer.
When you want to run it then you can start Pd on the RPI with the -nogui flag (see the command link above) which will help.
David.