Powering Arduino board from higher voltage source

I am working on building an off grid charge controller for my generator, which is a 10 HP engine running 2 130A alternators. The project is going good except for the max 12V input allowed to power the Arduino, during equalize charge the voltage is 15.5 - 16.2V on my battery bank which is too high for the Arduino. For the first few months it worked fine but then the regulator shorted out sending 12V through the usb cord and fried my computer as well when I was trying to figure out what failed.
Is there a simple way of adding an external regulator to these boards or an easy way to power it from the battery bank?

Yes. Search for buck converters. They are small and cheap.

I believe you experienced what is called load dump. They as you now know they are very nasty. The buck converter is a good choice but do not stop there, plan on protecting it from load dump and possibly reverse battery. There are diodes designed to help protect against load dump, the needed resistor is typically the wire feeding the module. Do some research on Load Dump and also look up Schaftner, they make the testers and there web sight use to have a lot of great information.