I haven't hooked my nook up to my computer in a while, but I believe you eject it just like you would a flash drive. If you have a PC with Windows 7, click the start button, then click computer and you should see your nook listed under Devices and Removable Storage. Right click the nook and click eject. That should be about it.
Here is more detailed info I found just in case you have an sd card in your nook.
Make sure to disconnect your nook from the computer correctly by using the "Eject" (in Windows, right click on the "nook" drive in My Computer and select "Eject" If you have an external microSD memory card in your nook, it will show up as a separate drive and you will need to Eject in this same way) or "Unmount" (Linux) command on the nook drive on your computer. If the nook is disconnected from your computer incorrectly, your sideloaded content may not be detected and displayed properly. If you want to read on your nook while it is connected to your computer for charging, you must Eject your nook and any external microSD memory card installed in your nook using the same process outlined above.