right now the river has some minor flooding, typical for this time year, will be rising due to more rain, snowmelt.
also, the river has a noticeable tidal influence south of middletown (and a bit north too) so you could end up paddling against the current.

https://water.weather.gov/ahps2/hydrograph.php?gage=mhdc3&wfo=box

The following is from a friend of mine:
Here are some web sites that I use:

https://tidesandcurrents.noaa.gov/noaatidepredictions.html?id=8463155
Select: Connecticut River -> Hadlyme

https://waterdata.usgs.gov/ct/nwis/current/?type=flow
Select: 01194750, CONNECTICUT RIVER AT ESSEX, CT

Of course the river is very tidal at Selden Neck. When I have camped there in mid May, there has never been a problem with tides flooding the camp sites, but end of April, that just might be a problem. What I would do is compare the high tides for a couple of days before you go with tides in mid May of 2018. If the high tides when you go are within a couple of feet of the high tides in mid May, I think you would be OK. Your bigger problem likely will be the river current, if you are paddling up or down river. The currents are affected by the tides, but probably more so by the increased flow of the river that we are currently experiencing, and I can find no web sites that show the flow rate that far south, where there are tidal effects. In addition if you get winds against your paddling, that might be a significant factor also. You would have to check weather forecasts for that. If you are a good paddler with a kayak, I would try it under most conditions. If you are paddling a canoe, you might have to seriously check the conditions, as a canoe can get wind bound much easier than a kayak. I would suggest that you put in the river at the Deep River town dock so you can paddle almost directly across the river, lessening the effects of wind and current.

If you have never camped on Selden Neck and are OK with primitive camping, you are in for a treat. Please do not miss the hiking on the island, especially the point of highest land, which gives you a magnificent view over the river to the west. There are lots of trails on the island. The height of land is toward the southern end. Just keep following a trail uphill.

I hope you enjoy!