The 48V will give you much better acceleration, hill climbing capability, etc.. overall better performance.
It will be more expensive since you will need to purchase a new 48V battery.
So my suggestion is to just buy a 36V/48V compatible controller for now, this way, you can just keep using your 36V battery until it dies.
When it's time for you to purchase a new battery, you can then decide whether or not you want the extra performance.
Good thing is that, your bike is a very generic ebike, there will be tons of 48V battery options available with different capacity.
Do you have a picture of your controller with wires / connectors on it?
If you don't, I'm asking because I'm wondering what you need to replace, depending on what connector you have.
Specifically, what kind of connector do you have on your:
- Battery (I'm talking about the connector that goes to controller)
- Motor inhibitor on brake
- Display (You will very likely need to replace this anyways, since your stock display doesn't do much and won't be compatible with the new controller)
- Cadence sensor (Your bike has cadence sensor yes? Not torque sensor)
- Motor (usually Z910, Z916 or L1019)