I've done a couple layover runs, but always with a friend who lives nearby, and never at an airport where I had to go through immigration/customs.
A four hour layover isn't actually that long. You may have 3 hours or less outside of the plane. Plan carefully to avoid wandering or wasting time. If you encounter any delays, you may need to abandon the run.
Where are you coming from/going to? Assuming you start in the US, you'll need to pass through immigration and customs before you can leave the airport. Depending on where you're going, you may need to go through immigration again when you return to the terminal. Obviously you'll also have to clear security on your way in.
Check most of your baggage through to your final destination, and carry on 1 small bag with you running stuff and whatever you want to bring on the plane. The smaller the bag, the easier it will be to stash. (You may need to research a bit and make sure it's possible to through check bags on your itinerary).
If you have access to an airline lounge, it likely has a shower. You can also ask them to hang on to your bag for a few hours (but they might say no). You can typically buy a one day pass to airline lounges, but it might cost $50.
Alternatively, you can shower and stash stuff at an airport hotel. Looks like Schiphol has one or two hotels in the terminal transit area, plus a few more on or near the airport grounds, one of which has a gym. You can definitely stash your stuff and shower there. Not sure how much it will cost.
You'll need to find the fastest route from the terminal to somewhere runnable. It may be possible start running at the terminal, but pedestrian access to airports is usually either poorly marked or non-existent.
Leaving Schiphol on a layover:
http://www.amsterdamtips.com/tips/amsterdam-airport-layover.php
Airport Sheraton with gym:
http://www.schiphol.nl/Travellers/Shop/ShoppingSchipholPlaza/Wellness.htm