I had no problem booking AS DCA/SEA this summer FC for 44K a ticket. Did it right of the website. Maybe EWR is the issue? Why not I believe AS flys both DCA and BOS so book a FC SEA or BOS and shuttle the wife to NY. It's no worse then a CLE stop and if its over a weekend you can pretty regulary snag a $170 shuttle fare if you have flexibility on DL ( maybe US but I would never put an expecting mother on US)

And by the waqy congrats on the expected new arrival.