There are two parts to a DC to DC converter/controller. The control logic that contains the feedback loop and control logic, and the switch, inductor/transformer or capacitors, diodes and resistors that comprise the converter/controller.
The terms can be synonymous, but when marketing IC's or modules it ususually comes down to these terms:
A controller usually contains all the logic and feedback loop, usually an IC nowadays and the rest of the DC to DC converter will need to be designed and passives added.
A converter usually contains everything needed for the DC to DC converter, and comes in a module form (or some IC modules, like the LTM's from linear).
The difference can be in the cost and ease of use, buying a module is much easier to integrate into a design, but it might not do everything you want it to. With a converter the input and output voltages, currents and power are fixed, and can't be changed.
With a controller, the designer can determine the input and output power, voltage by selecting different components. The switches can also be located outside of the part. The efficiency and cost can be determined by the designer by selecting different passives and switches (mosfets usually).
I've used both, more often than not a module doesn't have the power that I need in my products, so I'll design a DC to DC converter with an off the shelf controller.