Our Lady of the Rocks is the one sight on every Kotor boat listing that you can reach on your own for pocket change, so it is the honest comparison to run before booking anything.
The Blue Line bus leaves Kotor for Perast hourly through the day — from the main station four hundred metres south of the Old Town, or from the Riva stop in front of the walls — and takes about 35 minutes along the shore road. The fare is €2, cash to the driver; there is no advance booking and no online timetable worth trusting, because as every local guide puts it, the buses run on Montenegro time and fifteen to thirty minutes late is normal in July. It sets you down on the upper main road, and you walk down a flight of stone steps into the village.
From the Perast waterfront, local boatmen run the crossing to the island continuously in season, every half hour or so, seven to ten minutes each way. The going rate quoted by operators and visitors alike is around €5 to €10 return depending on the boatman and the month. Entry to the church and its small museum is collected on the island in cash, not by the boat crew: reports range from €2 for the museum to the €5 that Boat Taxi Kotor's own price guide states, so carry a note either way. Packaged versions exist — one Perast operator sells the round trip with the landing fee and entry bundled at €13 per person — and they exist precisely because the à la carte version confuses people.
So two people can be standing in front of Tripo Kokolja's baroque ceiling for roughly €8 of bus, €10 to €20 of boat and €4 to €10 of entry — call it €30 for the pair, with the whole afternoon in Perast attached. The cheapest guided alternative, the 90-minute Perast and Rocks run, is $29 each. On a straight price-per-head basis the bus wins, and it wins by more if you were going to spend the afternoon in Perast anyway.
What the bus does not buy is the reason most people book a boat at all. It does not reach the Blue Cave, which has no land access and sits an hour of open water away at the bay mouth. It does not reach the submarine tunnels on Luštica or Mamula. It gives you no swim stop, and it gives you no crossing of the Verige strait by water, which is the part of the day people photograph. The four-sight boats at $41 and $48 are not competing with a €2 bus ticket; they are selling the half of the bay that has no road.
The other public crossing worth knowing is the Kamenari–Lepetane ferry over the Verige strait, run by the state company JP Morsko dobro since it took the concession over. A car is €5, a motorcycle €2.50, a van €7.50, and anyone on foot or on a bicycle goes free — the same fare in season and out, cash at the booth. Under the summer plan it sails every 15 to 20 minutes around the clock, and the five-minute hop saves about 28 kilometres of driving round the head of the bay. It is not a sightseeing boat and it will not take you anywhere near the cave, but it is how you get to Tivat for the boats that leave from there without losing an hour to the shore road.