Nick Beer has made a nice command line tool for creating your own missions, including simple victory conditions and story. There are still many missing features and it isn’t particularly user friendly as it is now, as you can’t just run it and magic happens, but it is the first tool available in years for making missions that is also free to use! If I recall correctly all the previous tools have been payware and only available in German language.
Go ahead and download S2 Map2Mission and read how to set it up and use it!
As a side note: our online Map Generator does not currently support harbor generation. Adding the support is possible, but I’d rather make it “properly” instead of just quickly hacking it in. Doing it well makes it impossible for you to generate harbor maps that aren’t truly playable.