I can't seem to find out where the heater core hoses are on my 1990 4runner SR5 with the 3vz-e engine anyone know?

 

Pretty much smack center on the firewall at the top. Look for a pair of 5/8" hoses about 6 inches apart.

 

Do you know which one is Flow in and which one is Flow out?

 

The inlet side hose is connected to the heater control valve. It's a little black plastic box inline with the heater hoses. The outlet side runs back to the engine.

Also, you might be better off posting future questions about this truck in the 86-95 Truck/4Runner section.