I'm a corporate pilot so hopefully I can shed some light on this. However, I'm a little confused as to the actually arrangement of your travels. Hopefully this is a legitimate charter company (Part 135), not just some guy that owns an airplane and your company is paying him to fly you around (illegal). It could also be a fractional (Part 91k), but unlikely since the owner is actually flying the plane. Seriously, this is something you'll want to verify for your company.

Here's a breakdown

Part 91 - You or your company owns the airplane. Do what you feel necessary to keep your pilots happy. This is includes myself. I'm salaried and have never gotten cash tips, but I have been given bonuses for going above and beyond.

Part 91k Fractional - You own part of the plane and may see multiple different pilots throughout your travels. Tipping again isn't expected, but would be a generous way to reward good service.

Part 135 Charter - These guys are providing a service much like a taxi or limo driver. Tipping under these circumstances is more common, but not required. Don't tip through your broker. Your pilots will never see that money.

When tipping keep in mind:
-difficult weather that day (hot, cold, wind, fog, storms)
-friendliness of service
-cleanliness of cabin
-helping with bags, food, beverage
-type of equipment (prop, turboprop, jet)

If you decide to tip, I'd say a good tip range would be $20-$100 per pilot per trip. Longer trips you'll want to tack on a little extra. I have heard of pilots receiving well over $1000 in tips.

P.S. Keep in mind your average pilot may have payed as much as $100,000 to go through a collegiate flight school. It's not uncommon for co-pilots in these fields to be making as little as $20k/year. Also, do forget they probably have at least one ex-wife