I used to curse the tide or winds back when I paddled the marsh or tidal waters in my canoe, but I haven't found them as much of a problem since I bought my kayak. Unless you have one of the shorter river-type boats, most kayaks buck the wind and tide fairly well. I've even paddled long stretches upstream on many of the pine barrens rivers with mine with no problem.
Also, the further you are from the nearest inlet, the less problems the tides will give you. You will hardley notice a tidal flow on the tidal portion of the Wading River, but on Little Sheepshead Creek, close to the inlet, it will move you along quite swiftly.