It all depends on your definition of "best".

Navy pilots have to land on and routinely operate from an aircraft carrier.  Tough stuff.  But some USAF pilots have to operate 8 engine aircraft (B-52) and other "heavy iron", or operate routinely above 50,000 ft (U-2 and some others) wearing a full pressure suit.  USAF also operates stealth aircraft which have their own set of challenges.  On the other hand Army pilots routinely do nap-of-the-earth flying, routinely make dust and pinnacle landings, and operate in some very very austere locations.  Marine pilots do a mix of Navy flying and Army flying. 

Astronauts are about evenly divided between Naval Aviators (which includes Marines) and USAF aviators.  Only a very few Army aviators have become astronauts.  But is being an astronaut "flying" in any traditional sense?

So it all depends on your definition.

But being a Navy pilot myself, if I had to vote, you know what my vote would be.  ;-)