Comment Lots of Options (Score 1) 363
There are plenty of science museums throughout the country. The Association of Science - Technology Centers (ASTC) has more specific information, including a search engine, at http://www.astc.org/sciencecenters/find.php
These museums run a range from natural history (Academy of Natural Sciences in Philly), science museums for the general public (Boston's Museum of Science), Planetariums (Barlow Planetarium at UW Fox Valley), harder science museums (Harvard museum of Natural History, Woods Hole Oceanographic, National Renewable Energy Laboratory in Golden, CO), Transportation (North Carolina Transportation Museum), Aerospace (Virginia Air & Space Center), Medicine (International Museum of Surgical Science), botanical garden (Fairchild Tropical Botanic Gardens in Florida), and even a Presidential Library (McKinley's in Canton OH).
Similarly, it may be worth checking out the Association of Zoos and Aquariums, which other than having the obvious members, has a number of science centers included (Boston's MoS, California Science Center, etc.).
Beyond those, there are some obvious choices. The Smithsonian and other DC museums have plenty of geek options. 'Air and Space' (including the annex at Dulles) and Natural History are the 2 obvious ones. International Spy Museum is another. In Boston, you could include a campus tour of MIT along with the various local museums and the Mapparium. Any of the various NASA visitor centers across the country (Houston or Cape Canaveral are probably the best options of those). For just impressive engineering, the Hoover Damn, and the CN Tower (Yeah, technically Canada. Although if you're going from Boston or NYC to Chicago, that can be on the route). Also the Golden Gate, Willis Tower (formerly the Sears Tower), and Empire State Building, as well.
If you are interested in anatomy and physiology, you could look up where Body Worlds or Bodies: The Exhibition (or one of the competitors) is being exhibited.
Depending on when and where you go, you can also have the trip coincide with major SF/Fantasy conventions (Dragon*Con, PAX, GenCon, etc.).
Add in UCB Berkeley's Cyclotron, Oak Ridge National Laboratory, Spaceport America or Mojave Air and Space Port, an atomic museum (National Museum of Nuclear Science and History or Los Almos Historical Museum), and a pilgrimage to a Silicon Valley site (the Apple Museum?), and it should be fairly complete.