The place that offers the best chance for success on sea run browns is in the Allaire State Park section of the Manasquan River. I don’t know anything more specific than that but that’s where I always hear the fish are caught.
However, no one ever seems to know someone firsthand who has caught one but everyone seems to know someone who was told by someone that someone they knew caught an 8 lb sea run brown – but there’s never any substantiation. I did hear from speaking with one local fly shop in the area that there is indeed a limited number of sea run browns that happen in the fall/winter but you really have to know where, when and how to fish for them and there aren't many people who know the secrets and the ones that do aren't very forthcoming about it. It really sounds like a crap shot unless you know what you are doing.
As for the Connecticut River, I fished the Lake Francis outlet and the outlets from the First, Second and Third Connecticut Lakes many years ago. I don’t recall anything about sea run browns but there were landlocked salmon and I did hook into one ny mistake that probably went around 7-8lbs (on a 7.5 foot, 3 weight rod fishing a Mickey Finn for small brookies – it was gone before I knew what happened). Lots and lots of small brookies but there are a few decent sized ones as well. The upper reaches of the river is very tricky to fish in spots, as it’s not very wide but it is deep and in some spots you will be fishing while standing on top of giant boulders that drop off into 10+ feet of water. The water is crystal clear and you can actually see the fish holding on the bottom.
In addition to the Connecticut River, there are a lot of small, unnamed tribs in the area that offer excellent brookie fishing. Also, some of the best pickerel fishing I ever had was fishing the lily pads in some of the small ponds around the Pittsburgh, NH area.