IPhone – Stereo mic to iPhone 5S (jack) for recording

Just to be sure:

You mentioned checking the Sound control panel on the Macbook input side (I assume you selected Line In as well), but what about the output device on the Mac Mini? Plugging in the cable usually switches system output to Line Out, but not necessarily the output of whatever application you are using. So check both the Sound control panel output and the settings of your playback application (if it has any).

Also make sure the TOS connecter seats all the way (usually with a click). The Line In defaults to analog and, IIRC, it only switches to TOS if it senses a non-conductive plug clicking on some little switch.

What you are picking up is EMI from USB frame sync (most probably through the ground wire):

Every millisecond (12000 full-bandwidth bit times), the USB host transmits a special SOF (start of frame) token, containing an 11-bit incrementing frame number in place of a device address. This is used to synchronize isochronous data flows. High-bandwidth USB 2.0 devices receive 7 additional duplicate SOF tokens per frame, each introducing a 125 µs "microframe" (60000 high-bandwidth bit times each).

USB 2.0 added a PING token, which asks a device if it is ready to receive an OUT/DATA packet pair. The device responds with ACK, NAK, or STALL, as appropriate. This avoids the need to send the DATA packet if the device knows that it will just respond with NAK.

This could be avoided with a properly shielded extension cable. Note that even dockXtender only shields some of the wires:

A revolutionary 2-tier shielding system puts all video and audio signals inside a separate shielding to reduce interference from the other signals traveling through the wire.

If you're the DIY type of person it should be quite easy to make your own extension cable using high quality shielded wires. You will probably only need to connect just a few of the 30 pins: USB (power, gnd, data+/-), all GNDs and maybe accessory/serial (enable, rx/tx). Make sure you also shield the soldering on the connector.