Someone like Tagit can provide guru level info, but in general - yes.
Check out this thread posted in the past day or so:
http://www.fishing.net.nz/forum/fish-in-the-harbour_topic122789.html
Snapper push into the upper harbour from December until about April, feeding post spawning in the warmer water.
Good snapper can be caught in the shallows right up to Whenuapai, Te Atatu etc. It's light line fishing at dawn and dusk, lots of berley, casting well away from the boat.
in summer, you'll see heaps of boats anchored off Kauri Pt. But my instinct would be to try slightly out of the channel, or at least on the edge of it, where you don't need big sinkers to hold the bottom.
In terms of conditions, as Smudge says, it's when 15 knot plus wind opposes tide in high current areas that you'll have an uncomfortable trip. My desk at work overlooks the harbour opposite Stanley Pt and when the sou'wester is blowing down the harbour against an incoming tide, it cuts up very rough.
That area you're talking about is very exposed to SW. The Northcote ferry is often cancelled in those conditions.
Usually, you'll find that the SW (the prevailing wind in Auckland) kicks up late morning/afternoon in summer. you can get in a good trip from 6am till 10.30, certainly a feed. Another option would be to try off the North Shore's eastern coastline. There will be shelter from SW winds and in summer, there's some good fishing there I believe.