The steps outlined at Offensive Security's Nethunter wiki were incomplete or vague in some spots so I'm going to outline what worked for me. I'm using a 2013 Nexus 7 in my instructions.
Put your device in Developer Mode:
This is done by navigating to Settings -> About and tapping on the Build number field 7 times until you receive the notification that developer mode has been enabled. Go back to the main settings page and you will have a new section titled Developer options. Tap on the new Developer options section and enable both the Advanced Reboot and Android Debugging options.
Unlocking and Rooting Your Android Device:
For first time installations, it is usually best to completely flash your device "to stock" and bring it to a known-good state. This will ensure as painless an installation as possible, removing many of the variables that would cause an incomplete or failed installation. While there are many ways to unlock and root your Android devices, we chose to use the Windows based "Boot Rootkit" by WugFresh.
Download the Nexus Root Toolkit.
Download and install the NRT and execute it for the first time. Once loaded, click the Full Driver Installation Guide button. A Window with installation instructions will pop up – it is vital you read these instructions very carefully and follow them slowly. Once you have successfully completed a Full Driver Test in Step 4, proceed with the next step.
Flashing Back to Stock:
I found this post that said use Android 5.1.1 build LMY48M if you want to use Nethunter 3.0.
I used the NRT and chose Restore/Upgrade/Downgrade, and Device is on/Normal. I chose the build referenced above and let it download and install for me.
Now you need to go back and follow the steps above to unlock and root the device again. Make sure that "And also flash: Custom Recover" is checked.
Now download the appropriate Nethunter installation package from here. For my 2013 Nexus 7 running Android 5.1.1 build LMY48M I chose Nexus 7 2013 Lollipop. After its finished downloading, you need to copy it to the root of the Nexus file system.
Shutdown the device and hold down the power and volume down button it will boot into the boot loader. Use volume buttons to navigate to recovery and power to enter. After booting into recovery select install button,select the nethunter.zip swipe to flash and wait until it finishes. You'll be promted to install some packages. Choose the ones you want and accept the defaults. You can't go wrong here.
When it's finished, it will say "Zip Install Complete" near the top. Press the button to "Reboot System".
Enjoy Kali Nethunter on your Nexus 7!