Your right, Apple's docs on this are very XCode centric which doesn't really help for node-webkit. Luckily its actually pretty easy to do. Here are the steps:
(1) Obtain and Install your Developer ID certificate (this is the part that is well documented by apple):
(2) Make sure you have XCode and XCode developer tools installed
(3) From the Terminal run:
security find-identity
This will return something like:
Policy: X.509 Basic
Matching identities
1) SOME_REALLY_LONG_HASH "Developer ID Application: Your Name"
1 identities found
Valid identities only
1) SOME_REALLY_LONG_HASH "Developer ID Application: Your Name"
1 valid identities found
(4) Copy the really long hash into the following Terminal command as follows:
(5) Verify that it worked:
This should give you back the app details. You may notice that the identifier is com.intel.nw, if that is the case update your Info.plist file with the desired info, rebuild the app and resign it.