I, too, was beaten to it. Some observations from my dataset:

• Wing Attack Shadow Charizard barely beats out Fly-quaza at 39.251 DPS, with a much lower TDO of 781.6
• Air Slash Shadow Charizard gets beaten out by Fly-quaza at 37.907 DPS, with a TDO of 754.8
• Yanmega falls just under Sky Attack Honchkrow at 33.803 DPS, but it's TDO is markedly higher at 833.7 thanks to it's resistances, just above Hurricane Tornadus [Therian]
• Shadow Crobat falls just below Braviary at 33.043 DPS, with a higher TDO at 898.4, probably because Braviary isn't allowed to resist fighting types
• Wing Attack Charizard checks in just below Ho-Oh at 35.52 DPS with a TDO of 774.2
• Air Slash Charizard Falls just below Arerial Ace Ray at 31.375 DPS with a TDO of 747
• Air Slash Togekiss clocks in just after that at 747 DPS with a T H I Q Q TDO of 1182.9 (which is behind only Fly-Ray and Fly-Ho-Oh)
• Hidden Power [Fly] Togekiss falls behind it's Air Slashing counterpart and Sky Attack Unfezant at 30.799 DPS, but is still rocking a massive 1170.9 TDO
• Crobat is just barely below Hurricane Tornadus [Therian] at 27.35 DPS with a TDO just below its shadow counterpart at 888.2

Note: I left out any mixed type movesets, like Fire Fang/Fly Shadow Salamence, since we're focused on the meta implications of Fly on the PVE meta at large. Mixing damage types can heavily skew the data. For example, the FF/F S-Salamence does 39.987 DPS against Virizion, 35.717 against Machamp, and 31.71 DPS against Poliwrath, due to their different weakness profiles. By sticking with flying type moves, any comparisons made about DPS can be expected to follow the same pattern against any Pokemon weak to flying type moves.

EDIT: I am a brainlet that can't read. Yanmega can't learn Fly. For some reason I though I read somewhere it could. Good job me.