Neptune is a good program, and the bulk of the tuning is exactly the same no matter what software you use. There's not that many ways you can change a fuel map and set parameters. Don't feel too biased toward one or the other.
Either program would work fine for what you need; I would find a tuner that you feel good about and then ask them what they prefer and are comfortable with. It all boils down to the fact that the software isn't running in the ECU. The ECU doesn't care what software package made its program, it just wants a bunch of binary code to tell it what to do.