In regards to your being a new diver, yes Komodo can have some wicked currents, but that doesn't seem to stop any of the brand new divers I've run into with. If your comfortable underwater, hell why not? Your DM should take your experience in consideration, they see hoards of divers these days with very few dives. When I talk with a diver who has like 10 dives and they've been on a dive with 10 manta I tell them "might as well quit right now cause it doesn't get much better".
You can't swing a dead cat in Komodo without hitting another boat be it a LOB or dayboat out of LBJ. So you have plenty of options to choose. LOB'S cost a bit more than dayboats from LBJ but aren't as tiring and you can dive more of the park. There are LOBS in every price range, you get what you pay for. You can go from sleeping on deck with beer that gets warm on the third day cause its in a cooler to over the top luxury. Last year I slummed it on a budget LOB Weta Molas and it was suffecient but certainly not comfy. I went on it as it was going on a Southern trip and I can hardly get enough of Southern Komodo.
Another option which might be right up your alley is Scuba Junkies, they have a resort just outside the park in the central part of the park, and it's a bit cheaper than a budget LOB. It's a well run operation, a good value, and have a couple of accommodation options and the days are probably a bit shorter than diving out of LBJ. I've been to SJ 2x and recommend it over a dayboat out of LBJ.
Spend some time with Google and you'll find the choices overwhelming.
If you