The closest town to the Kelimutu Crater Lakes is Moni. Since the typical visit to the lakes is to see the sunrise, staying in the Moni area is the only alternative to traveling through the night on winding mountain roads.
There are only a few guesthouses and other accommodations in the immediate area of the multi-color lakes. Kelimutu Crater Lakes Eco Lodge is a new (opened July 2010) small hotel about 20 minutes from the park entrance. While it had its flaws when I stayed there, it's still probably the best bet. The other viable option in the Moni area is the Sao Ria Wisata Bungalows, but they don't seem to have a web site.