Yes. If both lights are controlled by two switches, then both switchs are a 3-way switch.
What you want to do is possible, but it may not be easy. The 3-way switches would be replaced by normal switches. You will have to likely run new wire to at least one of the lights and maybe have to run a new power wire to one of the switches (it all depends how it is currently wired). If the garage has an attic space that can be accessed, the wiring probably runs through there and it may or may not be able to be corrected from there. Some wiring may be in the walls and may be difficult to replace without drywall repair.
The way it is now, power comes from either switch, then probably goes to the overhead light, and then goes from there to the outside light. The problem is that outside light may not be directly connected to either switch (but it could be), so that is why I was saying that you would probably have to run some new wiring.
So, you have to think of how badly you want it this way and whether it would be worth it. If it is something you would like to do, you could get some quotes and an electrician could better see how things were run and how to make it work the way you want it.