its all a matter if you want a guide or not in the tour.
you mentioned reps. reps are not the only persons that can sell that tour.
its also available from local companies in the area. to make it simply:
plaka: boat to cross over-no guide
elounda: boat to cross over-i think with guide (local companies)
Agios Nikolaos: boats to cross over with guide (local companies)
Reps: boats to cross over with guide (they use local companies)

regarding price and how often i have no idea to inform you. if you are thinking to go just coz you read the book and think its a good idea then do it. but its a historical island that once upon a time it was a venetian fort and then a colony. so unless you want to walk around with no idea of what you see and the history do it from plaka. if you want to know the history do it from one of the other ways