What is the best way to travel from Crete to Patmos? What is the approximate travel time? Once in Patmos how would one get back to Naxos or Santorini? thanks!

Use www.gtp to figure out your travel times. You can get to Patmos from Mykonos, Syros, Kos and Rhodes. So if you're already on Crete you can take a ferry to Rhodes then another to Patmos. From Patmos you can take the ferry to Mykonos, and from Mykonos you can catch a ferry to Santorini and/or Naxos.

This will probably mean some overnights along the way unless you get very lucky with the connections, since some of these routes the ferries take aren't necessarily a daily occurrence.