Yes, you can use different weapons.
Nothing in the text of Extra Attack states which weapon or which hand or whatever you attack with, so you may attack with any weapon. If you are currently holding two weapons, you may attack once with one, once with the other.
You could also potentially attack with one weapon, drop it and draw another weapon with your free object interaction, and attack with that as your second attack. Nothing about Extra Attack says you are restricted even to weapons you are holding at the time (so long as you have the action economy necessary to grab more weapons; i.e. the free object interaction).