Yes there is a fair few flounder in the harbour. For flounder I suggest dragging the channels further up the harbour. For other fish I find the most consistent area is from the boat ramp straight across and out to the entrance. If you study a chart and fish the entrances of the smaller side channels on the changes of the tide you should do well.
Take Navonics on the phone and a fish finder with you if you can as there are a lot of sand banks in the harbour and its best to follow the main channels to your destination rather then going in a straight line. Avoids some embarrassment
The harbour fishes well all year if you are in the right spot at the right time. At the moment its inundated with ky from average to XL size and large gurnard. Snapper are still scarce but there is the odd large one around (lost a 15lb'er at the boat a couple of weeks ago). If the Raglan & the Kawhia reports on this forum are talking about good catches of snapper within the 30m mark out on the coast then the same kind of fishing can be found in the harbour.
December to June will also see the Kingi's and Trev's invade.