As well as several yacht and various classes of powered boat charters there appears to have been something of a proliferation of small boats for rent along the stretch from just past the Arsenali going East towards the sailing club. One details board (at least) that I saw offered three sizes of boat with only the largest one with a skipper specified. We spent a few nights in a harbour side hotel and I was checking some of the photos I took and some of the boats are featured. I even maneged to include a couple of phone numbers and web site.
You could try www.seasunribs.gr
+30 6932 459 125 and www.seaadventure.gr
+30 6944 3*66 643 (possibly 8 not 3) and from UK +30 6946 050 430.
Maud's down south but (assuming they're the same people and not two outfits with the same name) Notos also operate from Xania. I also know a man who runs cruised from Kissamos but I need to check his number as it seems he's moving the location of his other business in Xania and that's the number I have/had.
There's also been a boat offering cruises from Kalyves this summer. The boat carries about 20 people and they were offering 1 to 2 hour and ½ and whole day cruises on different days.