New Year's Eve gets very expensive in NYC. Everything has a cover, even the not-so-great bars, while the restaurants all have special menus that cost a lot.
We thought it might be nice to go with friends of ours to River Cafe for a low-key dinner. We were prepared for the $125 (still expensive, but worth it) prix fixe menu but when we called we were shocked to find out that the cost for New Year's was $450 per person, which includes a champagne and caviar cocktail hour. And can you believe it, it's completely booked as of this morning.
If you like seafood, one nice and well-priced option (in my opinion) is the Mermaid Inn. It's not in Brooklyn, but there is a location in the East Village and a new outpost on the Upper West Side. Here is a link to the menu. There are two seatings and the pricing is reflected ($50 & $70 menus).
Zagat offers a round-up of high-end prix fixe options, which does include the Mermaid Inn.