Hi Adam,
The small ferry connecting Samos (Pithagorio port) to Kalymnos is called “Nissos Kalymnos”. It’s indeed very hard to find any timetables online. From what I know it runs year-round, and the most recent timetable I found (on a Samos-based Greek site dated 11/2010) is the following:
From Samos (Pithagorio) to Kalymnos:
MON + FRI: Departs 16:15 (arrives 23.00)
WED + SUN: Departs 14:30 (arrives 21.00)
A slightly different timetable is listed here (http://www.nostalgia.gr/timetable-nissoskalymnos.html) but I cannot find a date anywhere, so who knows how old it is. What I would do is walk into a travel agency as soon as you arrive at Samos and ask — travel agents are usually the best informed.
I hope this helps!
Katie