Choices..
Thundermax, Sert, Harley race tunner, Daytona Twinteck, TTS Mastertune, Remus, S&S VFI, XIED's, Headquarters Pro tuner, Power Commander, to name but a few, and believe me the list goes on.
You can go from having a flash installed in you ECU from your local dealer to completely replacing your ECU, and everything in between, its a bit of a mine field and every one has there own idea of which one is best.
A couple of things to read.
Harley-Davidson Motorcycle Fuel Injection Explained Harley-Davidson Fuel Injection Upgrades