Inkaterra Reserva Amanzonica (Tambopata, Peru): Not only is the Amazonica one of the most luxurious camps in the lower Amazon, it's also one of the closest to Puerto Maldonado, where you will arrive by air. The Amazonica suites are gorgeous and have their own plunge pool and hammock. At night it's gas lamp only for a truly remote feel. If you aren't afraid of heights (I am!) check out their tree house room.
Inkaterra Machu Picchu Pueblo Hotel (Aguas Calientes, Peru): The perfect hotel base for exploring Machu PIcchu. The suites are super-comfortable, the food is good and their guides will take you on excursions beyond the ruins. Don't get sucked into the Sanctuary Lodge. Yes, it's at the ruins, but that does not outweigh the lack of comfort and ambiance you'll find at the Pueblo. Promise.
Costa del Sol (Lima Airport, Peu): If you arrive in Lima super-late and your next flight doesn't leave until the next day, stay at the Costa del Sol. It's literally across the street from International Arrivals and is a great place to get some quality sleep, shower and breakfast before continuing on your journey.