If you don't mind the transit time on the river, then there are some very nice marinas both above and below Middletown that you should investigate. This is where ActiveCaptain will be your best friend.
Midway marina in Haddam, CT is known for good winter storage rates, not sure about their summer rates. It's a real "boatyard", with an emphasis on repair services over fancy landscaping and pools. There are other marinas in the area that have those amenities.
With respect to mooring access and security, at my marina, the mooring rental includes in-water or land-based rack storage for your dinghy, whichever you prefer. I'm sure any other facility that rents moorings would provide space also. Some of the towns on the river will, for a fee, issue you a mooring permit, which allows you to place your own mooring subject to their guidelines for size and location. In that case, you may have to rely on the town's public access to launch and retrieve your dinghy. When I first moved to Saybrook, I used this method. After the harbormaster inspected my gear, I paid someone to place my mooring in the Ferry Point mooring field. After a few attempts to row the 1/2 mile from the public ramp to my mooring against a full moon tidal current in the river, I hustled over to the marina that was a predecessor to Island Cove and negotiated a deal for parking and dinghy storage for the season. It was a much easier trip coming out of the Ferry Point inlet and rowing across the current out to the mooring.
Security has not been an issue in recent years, but that's only because the caught the last knucklehead that was sneaking around at night raiding boats in the Essex/Old Saybrook area. It's always a risk, but frankly, someone with bad intentions would have an even easier time getting on my boat at the dock in the middle of the night when no one is around. Putting a security cam on the boat is on my to do list, but it's way down on the list!
