Rinca is a great place to see the Komodo Dragons. It is closer to Labuan Bajo and can be easily reached by boat in about 1.5 hours.
The visitor is a short walk from the dock and you can pay your entrance here. They will also assign a guide to take you on a hike to to see the Komodo. You can choose from a relatively short hike to longer half and full hikes.
The environment is quite arid for this part of the country. It is possible to spend the night here as several cabins are available for visitor accomodation. If you have time its a good option. I would check with the park headquaters directly in Labuan Bajo rather then booking through an agent.