The best place in Boston for dinner with a view has to be the Bay Tower Room, on 60 State Street's 33rd floor. Floor to ceiling windows look out over the harbor, the airport and right outside - seeming oversized because it's so close - the clock faces of the Custom House Tower. Reservations are a must. You want to control your visit so you arrive a half-hour before sunset. The room is terraced, so each table enjoys a nice view, but ask specifically for a table next to the window.
Start with a drink in the lounge, taking time to see the islands, harbor activity and planes coming into and taking off from Logan Airport as day gradually changes to night. As darkness takes over, the view shifts to city lights below.
The food is American with French tendencies. Most recently we had peanut crusted mahi mahi, an excellent choice, and the filet mignon, served with a rather thick French sauce which made the meal heavier than we would have liked. You should be able to find a current menu at link.
This is definitely a place for a splurge or to impress. And dress up! Jackets and ties for men, with appropriate equivalent for women. A piano or a trio plays soft jazz each evening and there is a small dance floor at one end of the lounge. It's not a place to hang out and dance - not at these prices - but if the mood strikes while you're here by all means go ahead.
Ah yes, the prices. The prices are the sole drawback. Bay Tower Room is at the high end of the scale, with appetizer meal and dessert it will be $40-50 per person. Add drinks and the tab builds. BUT go ahead and splurge... you only do this once, or for very special occasions. You should enjoy it.