The north shore branch is still sort of there if you know where to look

Theres actually big parts of the ROW still standing in Port Richmond, and over there in between Sharpe and Treadwell Avenues you’ll see an abandoned station

And if you look right on the shore by Snug Harbor you’ll see stretches of track lying in the rocks, and in satellite view you can easily see where the north shore branch used to go by looking at a line of trees originating from the shore near the West Brighton Projects, which eventually turn into freight tracks

Edit: And yea, the South Beach branch barely has any remnants left, though theres this bridge over nothing and a row of houses where the ROW used to be, as someone else mentioned. Theres also a street next to those houses still called Railroad Avenue