Versus an unknown this is grim.

Without putting it all into Equilab and in game I think I'm leaning towards a call. Even at these stakes people will over play weaker two pair combos so we're beating some of his value range at least some of the time.

His bet size is the worrying thing though. He knows that we can have 87s here, but he also knows that we raise a set on the turn most of the time so our most likely hand is weaker Ax that we can possibly fold to a 3rd barrel.

QJ and spade draws missed as well so it's all a bit murky

I'm going to sit on the fence and hope that @Komododragonjesus and @Harvie stop by

His bet sizing is kinda gross but I still think I click the call button. I do think villain could be going for value with worse, mainly A4, A9 (chop), maybe T9 or an overplayed AK. I don't expect A6 to pot turn so even though we beat that on the river I'm not really considering it.

This is a spot where he can have a bunch of bluffs like broadway draws, J8 J7 and flush draws plus maybe something like 86s deciding 6x is never good and continuing the bluff.

The trouble here comes with the question "how often is he bluffing" and the answer to that is I don't know. If he bluffs too much the answer is call, if he bluffs too little the answer is fold. I'm guessing villain is unknown since you didn't post any stats but even if we have a small amount of stats that still won't necessarily tell us what we need. In spots without info like this I tend to not fold near the top of my range (assuming your range is basically 44(maybe)-->AT-->A9-->etc).

Okay I wrote all that out and then plugged some #s into stove. This should be a megasnapcall. You need a little short of 33% for the call to be profitable getting over 2:1. Here's the equity stats if he has ZERO bluffs. Looks good, huh?

Board: As Ts 4h 9d 6c
Dead:

equity win tie pots won pots tied
Hand 0: 32.143% 25.00% 07.14% 14 4.00 { A9s }
Hand 1: 67.857% 60.71% 07.14% 34 4.00 { AA, TT, 44, ATs-A9s, A4s, T9s, 87s, ATo-A9o, A4o }

It's a tough one but vs an unknown I'm actually folding a bit more of these two pairs. You do beat AK, but also AT, TT, 44 may half pot and then when he thinks he has you pinned on the ace, they up the sizing.
87 I thought about but not sure how villain in general would cbet in two opponents. Though not terribly unlikely.

If they end up being a spazzy guy then you can get some good spots later, but vs unknown I think these folds can not be horrible. The pot bet sizes just lead me to lean toward them being a bit nuts but I don't know.