The scheduled boat and the archaeological site are sold by two different parties, and comparing a guided cruise against the cheap crossing means adding the second one in.
The crossing is run out of Deliana Pier by the Delos Tours boat owners at a published €25 return for adults, €12 for children aged six to twelve and free under six, sailing from the beginning of April to around the tenth of November. Departures run through the morning — the standard pattern is 09:00, 10:00 and 11:30, with an afternoon sailing in high season — and returns are timetabled in fixed pairs, so you get about three hours ashore in the morning or roughly two later. Entry is a separate €20 adult ticket, €10 reduced, sold on the island by the Ephorate of Antiquities of Cyclades and covering the ruins and the museum; EU citizens under 25 go free with photo ID.
So the cheapest way to stand in the House of the Dolphins is roughly €45 per person, and the $34 round-trip transfer here is the boat half of it, not the whole. Against that, the $102 cruise with lunch adds a licensed guide, the site ticket, a Rhenia swim stop and the food; the $159 all-inclusive version adds drinks and a smaller group. Delos Tours' own guided half day, sold at its pier office, is €79 with entry included — the reference point for judging whether a cruise price is doing any work.
What €45 does not buy is a swim. Swimming anywhere on the Delos coastline is prohibited, because the whole island is the protected site — the same reason nobody may stay overnight: around twenty guards and staff are the only people who sleep there, and every visitor leaves on the last boat. The swim on every Delos cruise happens at Rhenia, the uninhabited island across the strait, where boats anchor off and passengers go in from the ladder.
The same arithmetic runs on the south coast. Paradise, Super Paradise, Agrari and Elia all have KTEL services from Fabrika at €1.80 to €2.80, and the beach water taxi run by Mykonos Sea Transfer links Ornos, Platis Gialos, Paraga, Paradise, Super Paradise, Agrari and Elia on a €20 all-day hop-on pass with no single tickets. What neither buys is the coves with no road to them, the shade, the anchor time or the food — which is what the $115 yacht cruise and the $116 dinner cruise are selling.