I've done more than a dozen winter trips to Kona, mid-November through early April, ranging from 2 to 6 weeks in length. I'm in the dive shop nearly every day, and usually checking the manta reports among other things. I don't recall mantas being particularly unusual or episodic during those stays, though there was at least one stretch of several days or more with little action. Maybe winters are a little leaner for manta sightings, I don't go June-Oct.
I also recall only a handful of stretches lasting more than 2 days or so at a time of sufficiently high swells to shut us out of most of the shore-accessible sites. Days- to week-long runs of fairly flat water have been far more common. I would not at all characterize the Kona winter seas as typically rough, though the northern winter storms do affect conditions now and then. On the plus side, the trade winds are less in winter. I've heard it said that the Kona seas are actually flatter in winter, except when storm swells are coming through. Even then, it's not uncommon to hear of 20 ft seas on northshore Oahu while shore diving Kona stays very pleasant. Kona is somewhat shielded from north swells by Maui.
I don't do a whole lot of boat diving there but I often see where the big boats are going, and in my estimation they are fairly conservative about site selection. I've had them motor up to mooring buoys then move along elsewhere, because of what seems to me only a slight bit of surge. I go with Big Island Divers and cannot recall a trip that didn't have at least two very novice divers aboard. I suspect the big boat ops are all like that, it's mostly vacation clientele. Going with one of the smaller outfits might produce more opportunity. The manta dive is one where they are naturally going to be conservative, since you spend it sitting upright on the bottom.
There is definitely an annual sea temperature cycle, with the low in Feb-Mar. I don't know the stats but it's at least several degrees colder at that time, and from what I hear the low can vary quite a bit from year to year. One year it was almost undiveable in a 2.5mm fullsuit, but everyone said it was freakishly cold.