Wait a second. The problem is that the TARDIS can't go back to New York City in 1940 anymore, right? So why doesn't River go bring them back with her vortex manipulator? Sure, it's a bumpy ride, but Ten did it back when the Master took the TARDIS...
Alternatively, couldn't they just leave Manhattan then leave the Doctor a sign wherever they end up?
I don't know, did I miss something?
But seriously. I know it's a bit late for me to realize these things, but the end of the Angels Take Manhattan just keeps annoying me... it just felt like Moffat thought "Eh, they've been there too long, time to get rid of 'em... and make it look as touching and permanent as possible" and just threw something together.