Regardless of which school you apply to, take a careful look at what research the transportation professors do, and check them out on Web of Knowledge (access it through your current school's library page) and see when last they published something. I made the mistake of picking prestige over program and I'm ducking and running with a masters degree because I haven't learned anything. (I worked in transport planning/modeling/traffic engineering for nearly 4 years on three continents.)
Every class I've taken has been a Senior undergrad class, taught by a professor who is out of touch with the "real" world. There are no graduate-only transportation classes; well, they have some "on the books" but they haven't been taught as anything other than independent studies in probably decades. Three of the five transportation professors got their PhDs from the university; only one regularly publishes papers, and those tend to be in Environmental Management. The only research they do is actually GIS consulting, and the "Transportation Research Group" funds two Environmental Eng students while the Transportation students don't even get to work on what projects they do have going.
I go to a "Top 25" engineering school. The Environmental Engineering program is outstanding (if you're interested in the fate and transport of contaminents through porous media, it's non-existent if you're interested in water resources) and the Construction Management program is first class, as is the Risk and Reliability Engineering program (run by Structural Engineers). In terms of a Transportation education, however, I'd've been better off at a less prestigious State school.
