I know these are all ways to publish but is one better than the other and will anything need to be changed if i use another platform
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We use both PhoneGap and Cocoon, there is not much difference for OUR purposes.
One of our apps uses Cocoon Plugin for Construct 2 and we were to stupid to configure PhoneGap for that ^^ But Cocoon build works fine (not so surprisingly).
So it depends a bit on what exactly your project contains?
Phonegap has greater compatibility, causes less error, less lag. But the 2 are good, test your games on both, and then test again on other devices.
See the differences.