In the current Pokemon Champions regulation (Reg M-B) there are several Mega Charizard Y counters in terms of both megas and non-megas. Mega Charizard Y is viewed as the strongest mega, but it is far from unstoppable.
Mega Evolutions:
Mega Tyranitar can activate weather twice and is slower (better for weather abilities), meaning it generally stops solar beam and OHKOs back with Rock Slide, the most common move used to counter Mega Charizard Y.
Mega Raichu Y has not seen the most tournament success but enables some decent hyper-offense compositions. I have a great team featuring it with Dragapult, but that is not relevant to this question and I will try to post it on my accout if you would like to see it. It outspeeds Mega Charizard Y and can OHKO it.
Mega Delphox resist Fire, Grass, and Fairy type damage. It does not deal super effective damage to Mega Charizard Y, but has won tournaments recently when used as a fast counter that is also good into other common megas such as Floette.
Mega Dragalge is slow, but very bulky. It is highly reccomended to run Thunderbolt for damage into Mega Charizard Y and rain teams.
Non-Megas:
As you mentioned, Aerodactyl outspeeds Mega Charizard Y and OHKOs. The thing is, almost every rock type in the format does the same, with minor difference between their secondary roles. I will list a few of the more relevant rock types / Rock Slide users as well as non-rock types. Rock Slide can also almost always be substituted with Rock Tomb.
Garchomp is the most commonly used Pokemon that is also a counter to Mega Charizard Y. Life orb allows it to do insane damage and OHKO even bulky Charizard sets. It is two points faster than Mega Charizard Y and resists fire damage.
Kleavor can not only OHKO Mega Charizard Y, but also sets up stealth rock in the same turn that it attacks. This makes Mega Charizard Y take 50% of total maximum HP on switch. Use it if you also need a Farigiraf counter.
Lycanrock (Midday Form) is generally only seen on snow teams but can OHKO Charizard with a priority move.
Glimmora can be used as a mega, but is more often seen using the focus sash. Power gem is a special move, meaning intimidate does not weaken it. It is one point faster than Mega Charizard Y.
Toxapex is very bulky. It resists fire but is not weak to grass. It can trap Charizard and either use Toxic or have a team member deal with it.
Flash Fire uses can also work on the right team, not to do damage, but rather take hits for the team similar to Toxapex.
What not to use:
Mega Floette has a bad matchup into Charizard Y, given it resists your STAB attacks.
Rain teams seem like they would be good, but are limited by how easy it is for Charizard to overwrite weather. Mega Swampert deals good damage, but cannot take a Solar Beam at all.
