Slowly decreasing the speed on a steppermotor over time
millis() sound like a good way to go.

Check the estimated time until arrival (stopping), and in steps (you define yourself) you changen the (PWM) speed of the stepper motor.

Note, also for accelerating you can use the same step schema but reversed.

There are other ways, but I think those will be too complicated, like setting a (hardware) timer for the next speed change. Changing the speed in ms-accuracy will be more than enough. 

Do not use delay, since you still want to be responsive for pressed buttons, and (safety) sensors.