How funny! You've discovered another "feature" of ba.com... I too get told I can't book from NCL to EWR. However, there's good news:

You could make a BA Holidays booking for NCL to EWR by selecting flight+car on the webpage, but depending on how long you're away for it might work out more expensive.

You can also force ba.com to show you the flights by accepting the change to JFK, then clicking on the little "change" text towards the top of the page, and choosing NYC instead as a destination. It still gives you only JFK options at that point, but then click at the bottom of the outbound flights (for some reason it does give you the return options from EWR, just not outbound) on "more flight options", and you then get a list which includes EWR as a destination, and correctly quotes the price. Phew!

Alternatively, phone them up and get them to book it for you (and waive the fee, if possible, after they finished laughing when they discover that the website doesn't work for them either)

Good luck!