The only reason they had trouble beaming both Kirk & Sulu in freefall as well as Amanda was because the newly formed black hole was playing havoc with the targeting sensors. With Kirk & Sulu, Chekov had enough time to teleport them because he had a window of 25k feet (somewhere in that neighborhood), and he ONLY managed to teleport them RIGHT before they hit the ground. Amanda wasn't as lucky, as she was much closer to peril when the ground gave out beneath her.
That's why it was so much easier for them to beam Spock out of the Jellyfish before he hit the Narada, because they didn't have to contend with anything that would impede their sensors. Also, the drill hadn't been turned on by the time Kirk and Spock beamed onto the Narada.