I did Komodo in August on the Arenui. Beautiful boat and we had mantas. The islands were very brown and I got the feeling that it was normal for the area rather than seasonal. I found the domestic flights to be easy and stress-free.
My shots from the trip are here: http://lizrogersphot...com/tag/komodo/
The last article on that page has a video which is my underwater shots and cruise co-ordinator Eduardo's aerial drone shots.
I also saw a mola mola in Tulamben in Bali last Christmas. Unfortunately it was at 100m so this may not be useful information...but they are in the area all year round.