Keeping Stealth Rock up really helps.
Moltres is a very hard Pokemon to counter, often you have to resort to pivoting around its attacks to beat it. For example, let's say you have a Hitmonchan out, you can switch to a resist to the expected Air Slash, such as Omastar, then switch to something that can revenge it that doesn't really care about the attack. In this case it'd be HP Grass, so you'd switch to something such like Rotom who doesn't take that much from HP Grass, is faster than Moltres, and can OHKO it, or something such as HP Rock Sceptile. There are quite a lot of Pokemon who outspeed Moltres, too.
A lot of Pokemon were mentioned in this thread already, so I'll name some lesser used options for beating Moltres:
Support Clefable
ParaShuffler Druddigon
Stunfisk (beware it takes a ton from LO Fire Blast)
Defensive Altaria
"Mootility"
There are other options out there, these are just a few! I wish you luck, and if you find any interesting Moltres checks/counters please share them! :)