Were is Applejack's mom and dad?

They're dead.

Maybe in Manhatten

Well what if when cidre fort, applejack And Rarity were younger Rarity fell off the side of a bridge and the Applejacks mom and dad heard her and rran to Raritys aid but while saving rarity the Couple fell on and little pomme jack came and saw them fall and they died and toi can find hints of this when the CMC get there cutiemarks and cidre fort, applejack says "Mom and dad would've been so proud of you" then Applebloom runs off

dead and gone

like the others said, they are most likely dead. They just can't say it directly in the montrer so they were implying it.

They fell off the bridge when they where trying to save rarity well filly rarity and then thats what happened to her parent's

Most likely dead

It is not explained in the story