There are really two bases — the village you can walk around, and the boat-drop lodges strung south along the coast — and the difference is whether you can choose where you eat.
Agujitas — the village, and the only walkable base
The settlement at the mouth of the Río Agujitas has the sodas, the pulperías, the cheapest rooms and the beach the passenger boats land on. If you want to be able to walk somewhere and pick your own dinner, this is the only option.
The coast south towards Punta Marenco and San Josecito
Lodges spaced along the shore and the coastal trail, most reached only by boat, all quoting per person with meals included. You are paying for isolation and for being closer to the edge of Corcovado; the cost is that you are committed to one kitchen and one set of departure times.
Understand what an all-inclusive rate means here
Almost everything outside the village quotes per person per night with three meals and boat transfers folded in, because there is no road and nowhere else to eat once the boat has gone. Compare rates on that basis rather than against a room-only price elsewhere, or Drake Bay looks far more expensive than it is.
Practical: sleep in Sierpe the night before
The boat down the river leaves Sierpe late morning, so an overnight in Sierpe saves a pre-dawn start from San José or the airport and removes the risk of missing it. Sierpe is the last town on the road, with hotels and restaurants; Drake has neither road nor spare seats.