as I've heard that the ferry doesn't run in September.
well you are right and not right at the same time - the 'water tram' (it's not a ferry - no cars allowed) from Gdańsk to Hel does not run in Sept - however the connection from Gdynia to Hel runs in September - there is only one course - it departs at 10 am from the port in Gdynia and arrives at 11am in Hel the return course departs at 3pm from Hel and arrives at 4pm in Gdynia (Gdynia is part of the Tricity)
however the transfers to port in Gdynia can prove problematic to you
the alternative connection is a railway connection - however you still need to change in Gdynia Główna - you first need to take a train from Gdańsk Główny (Gdańsk Central Station) to Gdynia Główna - there are plenty of trains between them - you can use SKM city trains but be sure to buy a ticket for it before you board - from Gdynia you got direct trains to Hel like every 2 hours during the daytime