What's your definition of 'nice'? What kind of experience are you looking for? Price range? Off the top of my head, here's a list of places I find to have top teir food and offer an excellent overall dining experience. They all tend to be 'fancy' and expensive however and might be more suitable to dates than to dinners with 16yo nieces... depending on what you're after.
No. 9 Park - French/Italian. I'd only go for their prix fixe menu which the couple times I've had it was quite good. I'm particularly fond of the prix fixe format as culinary experience though.
Radius - French/Fusion. The food is both very good and a bit unique.
Capital Grille - Steak. Probably the best - and most expensive - steak in Boston.
Federalist - American. Fresh, inventive food and a chocolate/raspberry, mousse-like cake that must be the work of the devil.