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. ;-)