If was shore diving for two days, I'd do the Place of Refuge one day and Puako the other day...if conditions allowed (I see you're planning on coming over at the end of January, and shore diving may or may not be good then... it's all dependent on the swell of the day).
If you're boat diving, you might get some input, but unless you rent out the whole boat and the sites are available and diveable you might not get a specific site. Most operators here are going to do their best to show you a site with good conditions that offer something the majority of their divers are going to want to see.
I'd definitely recommend trying to get the manta dive in if conditions are decent and the mantas are coming in at the time. As far as day dive sites go, Kona's got a lot of good ones and anyone who dives here a lot will likely have 8-10 favorites so you should have a lot to choose from.
Have fun,