If BootFailure is being run, obviously something broke during boot, so why are we running code that blithely assumes Jenkins.getInstance() is non-null (and servletContext valid) without doing a null check?
And why are we even using Jenkins.getInstance().servletContext? BootFailure.publish already has a ServletContext! It should just pass it to the GroovyHookScript.
High priority IMO since when this happens, it means there was a fatal error that blocked Jenkins from starting…but that error is completely lost because this NPE is printed instead.
I would suggest that LOGGER.log(SEVERE, "Failed to initialize Jenkins",e); be run even in case of BootFailure, just to be sure that the root cause is never lost.