Martin Travel has been doing receptive work out of Asunción since 1986, first as Intertours and under the present name since 2009, and they have an office in Foz do Iguaçu as well as the one in Asunción. They will guide in Spanish, English, German or Portuguese, which in Paraguay is less common than it sounds.
Their day tours are the two you actually want from Asunción. The Circuito de Oro runs about seven hours daily and takes in Itá and its lucky clay hens, the eighteenth-century Franciscan church at Yaguarón, Piribebuy, the basilica at Caacupé, lunch at San Bernardino on Lago Ypacaraí, and Itauguá for ñandutí lace on the way back. Lunch is included, drinks are not.
The full-day Jesuit missions run is honest about what it costs you: the bus leaves Asunción at 00:30, you reach Encarnación for breakfast, see Trinidad and Jesús de Tavarangüé, and come back on the 18:00 bus. It is a long day and they say so on the page. If you would rather not do it in one, their multi-day programmes string Asunción, the missions and Iguazú together over six or seven days.
No prices are published; they sell through agents as much as direct, so ask.