Got it. If you're doing fall/spring, then any of the destinations are game, IMHO.

For NYC - If you've never been to the city before, I'd recommend Top of the Rock or top of the Empire State Building, the ferry to the Statue of Liberty and Ellis Island, and strolling Central Park and/or the High Line (free) to start. You can grab theatre tickets at the TKTS booth for deep discount Broadway tickets. I also just love going to Grand Central Station and watching it fill up and empty again. (There's a great food court there with yummy, inexpensive options.) Also, there are several NYC museums that are free, so if you have bad weather, you can duck into one of those.

For Boston - Trinity Church and the Boston Public Library are free. So is Boston Public Garden, Boston Commons, and the Granary Burying Ground. It's worth paying to get into the JFK Memorial Library/Museum and the Isabella Stewart Gardner Museum. If you're into sports and beer, you can tour Fenway and the Sam Adams Brewery. We also loved Fanueil Hall (free), the Old North Church (cheap), and the Revere House. Lastly, you can climb the Bunker Hill monument and then get eats in nearby Little Italy.

For Atlanta - I'd hit Centennial Olympic Park (free) and their big Ferris wheel. I also love their botanic garden, and you should spend time at the King Center (MLK's childhood home, the church where he preached, and corresponding museum/garden). The High Museum of Art is wonderful, and I really enjoyed the Center for Puppetry Arts. (Miss Piggy, Kermit, the Fraggles - they are all here, in addition to puppets from different cultures.) Oakland Cemetery (free) has some cool historic graves, and you can just browse and snack at Ponce City Market. If there's a show at the Fox Theatre, you can catch that, and if you're a history buff, you can visit the Jimmy Carter Presidential Library. (There was so much about him that I didn't know.) If you're into touring, you can tour CNN and/or the World Coca-Cola Museum.