Gyp is pretty nice but the documentation is awful.
The answer in case anyone runs across the need for it is:
'xcode_settings': {
'GCC_PREFIX_HEADER': 'path/from/gyp/file/to/header.h',
'GCC_PRECOMPILE_PREFIX_HEADER': 'YES',
},
Also worth noting you can set pretty much everything in this page in a xcode_settings block