There are literally hundreds of boats that do day cruises/tours leaving from the city dock. They all go to more or less the same places, same beaches and swimming spots. It is like a large convoy of boats, all leap-frogging to the same beaches for their 30 minute stops.
Unique Suggestions: If you will be in town for more than a day, I highly recommend that you walk the dock a day before to scout the boats. Some are large, some are tiny. Some will crowd you in with a couple hundred people and if you do not arrive ~90 minutes before departure, you will not have a comfortable seat.
I recommend that you choose a boat that suits your personal taste and then make your booking for the following day. Most of the boats will be returning to the dock around sunset, so arrive a few minutes before then to see what the crowds are like.
Fun Alternatives: If you do not like crowds, then go to the beaches instead since you will have more personal space to relax. However if you like the boats and the crowds do not bother you, enjoy!
If you arrive early in the morning and nothing is open yet to get an awakening cup of coffee, try to avoid this “panificadora” that opens first.... . Everything is awful, coffee is the worst I have tasted in Brazil. The sandwiches taste bad and all of us had problems after having breakfast there, even those who had a sandwich only with cheese...
It is located in Praca do Chafariz.
Well, visiting Paraty with flip-flops is the dumbest thing to be done. The pavement is covered with 18th Century rocks, a hard slave work. It's beautiful, but, to walk, it's not the best floor. With flip-flops, the probability you have of falling down is 50-50. If the rocks were wet, this proportion increases dramatically. Take your tennis.
Unique Suggestions: If you reach downtown and find you forgot to let your flip-flops at the hotel, hold your flip-flops, or put them in a bag, and walk with bare feet. It's less dangerous (take care with dogs "works").
Fun Alternatives: Well, bare feet walking. Choose always the "sidewalks" or the central part of the rock floor to walk by; these parts are less irregular.