Yeah unless you have enough in your group to book the whole plane, the flights to Ica then small plane over Nazca aren't an option from Lima. I tried this through several companies, including my hotel. Basically, I was put on a "list" that all hotels, travel agencies, etc were feeding into. And if the pilot could fill the plane to make the trip cost efficient, the trip would proceed. If not (as in my case), they would cancel and refund all monies (around $USD500 for the day trip).
You can - if you have spare time and don't mind giving it a shot with no guarantees - head to Ica on Aerocondor, and once there hope to round up enough strangers to convince a pilot to run you on the small plane over the Lines. Or there's always the overland route which can run anywhere from around $100-300 USD (depending on what all the tour operator includes).
i'm a loser and never made it there since I had to unexpectedly cut my Lima trip short by a day and couldn't spare the "waiting and hoping" time. So this means another trip to Peru is in order!